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Lead in PDB 5gpe: Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)

Protein crystallography data

The structure of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II), PDB code: 5gpe was solved by S.Q.Huang, W.Z.Chen, D.Wang, Q.Y.Hu, X.C.Liu, J.H.Gan, H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.938, 67.903, 89.723, 109.33, 89.82, 90.32
R / Rfree (%) 17.7 / 21.4

Lead Binding Sites:

The binding sites of Lead atom in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) (pdb code 5gpe). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 8 binding sites of Lead where determined in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II), PDB code: 5gpe:
Jump to Lead binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Lead binding site 1 out of 8 in 5gpe

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Lead binding site 1 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pb201

b:29.8
occ:1.00
 SG B:CYS113 2.7 29.8 1.0
SG A:CYS78 2.7 28.2 1.0
SG B:CYS122 2.8 24.3 1.0
O A:CYS78 3.2 22.5 1.0
OD1 A:ASN82 3.3 24.6 1.0
CB A:CYS78 3.4 26.4 1.0
CB B:CYS113 3.5 30.0 1.0
ND2 A:ASN82 3.6 26.2 1.0
CG A:ASN82 3.7 24.4 1.0
CB B:CYS122 3.8 23.4 1.0
C A:CYS78 3.9 26.5 1.0
CB A:VAL81 4.0 22.4 1.0
CA A:CYS78 4.3 26.4 1.0
CA B:CYS122 4.3 25.6 1.0
CG1 A:VAL81 4.4 24.9 1.0
N A:ASN82 4.4 19.2 1.0
CD1 B:ILE124 4.5 24.7 1.0
N B:GLY123 4.7 25.7 1.0
CB A:ASN82 4.8 22.2 1.0
N A:GLY79 4.8 23.7 1.0
CG2 A:VAL81 4.8 22.8 1.0
C B:CYS122 4.9 24.9 1.0
CG1 B:ILE124 4.9 23.6 1.0
CB B:ILE124 4.9 23.1 1.0
CA B:CYS113 4.9 29.1 1.0
C A:VAL81 5.0 19.8 1.0
CA A:VAL81 5.0 21.8 1.0
CA A:ASN82 5.0 20.9 1.0

Lead binding site 2 out of 8 in 5gpe

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Lead binding site 2 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pb201

b:23.5
occ:1.00
 SG B:CYS78 2.6 17.8 1.0
SG A:CYS113 2.7 19.3 1.0
SG A:CYS122 2.8 19.0 1.0
O B:CYS78 3.2 19.9 1.0
CB B:CYS78 3.4 18.9 1.0
OD1 B:ASN82 3.4 23.8 1.0
CB A:CYS113 3.5 19.7 1.0
ND2 B:ASN82 3.7 23.1 1.0
CG B:ASN82 3.8 21.6 1.0
CB A:CYS122 3.8 20.9 1.0
C B:CYS78 3.9 20.0 1.0
CB B:VAL81 4.0 17.1 1.0
CA B:CYS78 4.2 19.9 1.0
CA A:CYS122 4.3 19.7 1.0
CG1 B:VAL81 4.3 17.2 1.0
N B:ASN82 4.4 17.0 1.0
CD1 A:ILE124 4.4 19.6 1.0
O A:HOH330 4.5 22.2 1.0
O A:ASP114 4.6 34.5 1.0
N A:GLY123 4.7 16.2 1.0
CG2 B:VAL81 4.8 18.1 1.0
N B:GLY79 4.8 19.5 1.0
C A:CYS122 4.9 17.8 1.0
CB B:ASN82 4.9 19.9 1.0
CB A:ILE124 4.9 18.5 1.0
CG1 A:ILE124 4.9 19.2 1.0
CA A:CYS113 5.0 23.2 1.0
N A:ILE124 5.0 18.6 1.0

Lead binding site 3 out of 8 in 5gpe

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Lead binding site 3 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pb201

b:23.4
occ:1.00
 SG C:CYS78 2.6 20.7 1.0
SG D:CYS113 2.7 22.7 1.0
SG D:CYS122 2.7 19.8 1.0
O C:CYS78 3.3 18.4 1.0
OD1 C:ASN82 3.4 25.2 1.0
CB C:CYS78 3.4 18.9 1.0
CB D:CYS113 3.5 21.6 1.0
CG C:ASN82 3.7 22.3 1.0
ND2 C:ASN82 3.8 22.8 1.0
CB D:CYS122 3.8 21.1 1.0
C C:CYS78 3.9 20.5 1.0
CB C:VAL81 4.0 19.1 1.0
CA D:CYS122 4.3 20.1 1.0
CA C:CYS78 4.3 20.1 1.0
CG1 C:VAL81 4.3 19.8 1.0
CD1 D:ILE124 4.4 21.3 1.0
N C:ASN82 4.4 14.9 1.0
O D:HOH333 4.5 21.4 1.0
O D:ASP114 4.6 28.0 1.0
N D:GLY123 4.7 17.5 1.0
CG2 C:VAL81 4.8 20.1 1.0
CG1 D:ILE124 4.9 20.6 1.0
CB D:ILE124 4.9 19.1 1.0
C D:CYS122 4.9 18.0 1.0
N C:GLY79 4.9 21.3 1.0
CB C:ASN82 4.9 20.1 1.0
CA D:CYS113 4.9 23.5 1.0
N D:ILE124 5.0 18.6 1.0

Lead binding site 4 out of 8 in 5gpe

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Lead binding site 4 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pb201

b:29.4
occ:1.00
 SG C:CYS113 2.6 28.8 1.0
SG D:CYS78 2.7 28.2 1.0
SG C:CYS122 2.8 24.1 1.0
O D:CYS78 3.2 22.4 1.0
OD1 D:ASN82 3.3 24.8 1.0
CB C:CYS113 3.5 30.4 1.0
CB D:CYS78 3.5 26.7 1.0
ND2 D:ASN82 3.6 30.8 1.0
CG D:ASN82 3.7 25.9 1.0
CB C:CYS122 3.8 25.5 1.0
C D:CYS78 3.9 25.0 1.0
CB D:VAL81 4.0 21.3 1.0
CA C:CYS122 4.3 27.3 1.0
CA D:CYS78 4.3 25.2 1.0
N D:ASN82 4.4 21.6 1.0
CG1 D:VAL81 4.4 22.5 1.0
CD1 C:ILE124 4.4 28.4 1.0
N C:GLY123 4.7 24.9 1.0
CB D:ASN82 4.8 22.6 1.0
N D:GLY79 4.8 23.8 1.0
CG2 D:VAL81 4.8 21.2 1.0
C C:CYS122 4.9 26.0 1.0
CG1 C:ILE124 4.9 26.2 1.0
CA C:CYS113 4.9 31.5 1.0
CB C:ILE124 4.9 23.9 1.0
C D:VAL81 5.0 20.7 1.0
CA D:ASN82 5.0 22.0 1.0
CA D:VAL81 5.0 21.5 1.0

Lead binding site 5 out of 8 in 5gpe

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Lead binding site 5 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 5 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Pb201

b:30.4
occ:1.00
 SG F:CYS113 2.6 29.2 1.0
SG E:CYS78 2.7 26.4 1.0
SG F:CYS122 2.8 23.4 1.0
O E:CYS78 3.2 22.9 1.0
OD1 E:ASN82 3.3 26.2 1.0
CB F:CYS113 3.4 31.4 1.0
CB E:CYS78 3.5 26.2 1.0
ND2 E:ASN82 3.7 30.9 1.0
CG E:ASN82 3.7 25.8 1.0
CB F:CYS122 3.8 23.1 1.0
C E:CYS78 3.9 25.9 1.0
CB E:VAL81 4.0 22.8 1.0
CA F:CYS122 4.3 24.9 1.0
CA E:CYS78 4.3 26.0 1.0
CG1 E:VAL81 4.3 24.7 1.0
N E:ASN82 4.3 18.5 1.0
CD1 F:ILE124 4.4 24.1 1.0
N F:GLY123 4.7 24.9 1.0
CB E:ASN82 4.8 23.2 1.0
CG2 E:VAL81 4.8 23.4 1.0
N E:GLY79 4.8 23.7 1.0
C F:CYS122 4.9 24.4 1.0
CA F:CYS113 4.9 30.0 1.0
CG1 F:ILE124 4.9 23.8 1.0
CB F:ILE124 4.9 22.8 1.0
C E:VAL81 5.0 21.4 1.0
N F:ILE124 5.0 22.8 1.0
CA E:VAL81 5.0 22.3 1.0
CA E:ASN82 5.0 22.4 1.0

Lead binding site 6 out of 8 in 5gpe

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Lead binding site 6 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 6 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Pb201

b:23.4
occ:1.00
 SG F:CYS78 2.6 20.4 1.0
SG E:CYS113 2.7 22.9 1.0
SG E:CYS122 2.8 17.8 1.0
O F:CYS78 3.3 20.0 1.0
OD1 F:ASN82 3.4 24.2 1.0
CB F:CYS78 3.4 18.9 1.0
CB E:CYS113 3.5 21.6 1.0
ND2 F:ASN82 3.7 23.2 1.0
CG F:ASN82 3.7 21.7 1.0
CB E:CYS122 3.8 20.4 1.0
C F:CYS78 3.9 20.3 1.0
CB F:VAL81 4.0 17.0 1.0
CA F:CYS78 4.3 20.5 1.0
CA E:CYS122 4.3 19.7 1.0
CG1 F:VAL81 4.3 17.9 1.0
CD1 E:ILE124 4.4 23.1 1.0
N F:ASN82 4.4 16.3 1.0
O E:HOH336 4.5 27.2 1.0
O E:ASP114 4.6 31.8 1.0
N E:GLY123 4.7 17.5 1.0
CG2 F:VAL81 4.8 17.4 1.0
CG1 E:ILE124 4.9 20.4 1.0
CB E:ILE124 4.9 18.4 1.0
N F:GLY79 4.9 20.5 1.0
CB F:ASN82 4.9 19.5 1.0
C E:CYS122 4.9 17.8 1.0
CA E:CYS113 4.9 23.7 1.0
N E:ILE124 5.0 16.9 1.0

Lead binding site 7 out of 8 in 5gpe

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Lead binding site 7 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 7 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Pb201

b:29.6
occ:1.00
 SG H:CYS113 2.6 28.9 1.0
SG G:CYS78 2.7 28.0 1.0
SG H:CYS122 2.8 24.4 1.0
O G:CYS78 3.2 21.6 1.0
OD1 G:ASN82 3.3 24.3 1.0
CB H:CYS113 3.4 30.3 1.0
CB G:CYS78 3.5 28.2 1.0
ND2 G:ASN82 3.6 27.6 1.0
CG G:ASN82 3.7 23.9 1.0
CB H:CYS122 3.8 24.6 1.0
C G:CYS78 3.9 23.7 1.0
CB G:VAL81 4.0 21.3 1.0
CA H:CYS122 4.3 25.8 1.0
CA G:CYS78 4.3 25.7 1.0
CG1 G:VAL81 4.4 23.0 1.0
N G:ASN82 4.4 20.4 1.0
CD1 H:ILE124 4.5 27.3 1.0
N H:GLY123 4.7 23.4 1.0
CB G:ASN82 4.8 22.1 1.0
N G:GLY79 4.8 20.6 1.0
CG2 G:VAL81 4.8 21.5 1.0
C H:CYS122 4.9 25.0 1.0
CA H:CYS113 4.9 29.4 1.0
CG1 H:ILE124 4.9 24.3 1.0
CB H:ILE124 4.9 23.1 1.0
C G:VAL81 5.0 20.2 1.0
CA G:VAL81 5.0 21.3 1.0
N H:ILE124 5.0 23.4 1.0
CA G:ASN82 5.0 21.1 1.0

Lead binding site 8 out of 8 in 5gpe

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Lead binding site 8 out of 8 in the Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II)


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 8 of Crystal Structure of the Transcription Regulator PBRR691 From Ralstonia Metallidurans CH34 in Complex with Lead(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Pb201

b:23.4
occ:1.00
 SG H:CYS78 2.6 18.5 1.0
SG G:CYS113 2.7 17.8 1.0
SG G:CYS122 2.8 19.1 1.0
O H:CYS78 3.2 22.2 1.0
OD1 H:ASN82 3.4 24.1 1.0
CB H:CYS78 3.4 18.4 1.0
CB G:CYS113 3.5 20.4 1.0
ND2 H:ASN82 3.7 22.2 1.0
CG H:ASN82 3.7 21.2 1.0
CB G:CYS122 3.8 21.0 1.0
C H:CYS78 3.9 19.9 1.0
CB H:VAL81 4.0 18.5 1.0
CA H:CYS78 4.3 18.9 1.0
CA G:CYS122 4.3 19.8 1.0
CG1 H:VAL81 4.3 18.5 1.0
N H:ASN82 4.4 17.5 1.0
CD1 G:ILE124 4.4 21.1 1.0
O G:ASP114 4.5 28.4 1.0
O G:HOH326 4.6 22.4 1.0
N G:GLY123 4.7 17.1 1.0
CG2 H:VAL81 4.8 19.4 1.0
N H:GLY79 4.9 19.7 1.0
C G:CYS122 4.9 18.1 1.0
CB H:ASN82 4.9 19.6 1.0
CG1 G:ILE124 4.9 20.1 1.0
CB G:ILE124 4.9 19.1 1.0
CA G:CYS113 4.9 22.0 1.0
N G:ILE124 5.0 17.7 1.0

Reference:

S.Q.Huang, X.C.Liu, D.Wang, W.Z.Chen, Q.Y.Hu, T.B.Wei, W.Q.Zhou, J.H.Gan, H.Chen. Structural Basis For the Selective Pb(II) Recognition of Metalloregulatory Protein PBRR691 Inorg Chem V. 55 12516 2016.
ISSN: ISSN 1520-510X
PubMed: 27989185
DOI: 10.1021/ACS.INORGCHEM.6B02397
Page generated: Thu Oct 10 10:09:26 2024

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