Atomistry » Zinc » PDB 2pop-2q1q » 2pve
Atomistry »
  Zinc »
    PDB 2pop-2q1q »
      2pve »

Zinc in PDB 2pve: uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin

Protein crystallography data

The structure of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin, PDB code: 2pve was solved by D.M.Lemaster, J.S.Anderson, L.Wang, Y.Guo, H.Li, G.Hernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 0.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.169, 56.860, 38.170, 90.00, 112.92, 90.00
R / Rfree (%) 11.2 / 12.5

Zinc Binding Sites:

The binding sites of Zinc atom in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin (pdb code 2pve). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin, PDB code: 2pve:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pve

Go back to Zinc Binding Sites List in 2pve
Zinc binding site 1 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:5.5
occ:1.00
SG A:CYS9 2.3 5.5 1.0
SG A:CYS42 2.3 6.2 1.0
SG A:CYS6 2.3 5.7 1.0
SG A:CYS39 2.4 5.5 1.0
HB3 A:CYS9 3.1 6.4 1.0
HB3 A:CYS6 3.1 7.0 1.0
H A:CYS42 3.1 8.0 1.0
CB A:CYS6 3.2 5.8 1.0
HB3 A:CYS39 3.2 6.7 1.0
CB A:CYS39 3.2 5.6 1.0
H A:CYS9 3.2 6.6 1.0
HB2 A:CYS39 3.2 6.7 1.0
HB3 A:CYS42 3.2 8.2 1.0
HB2 A:CYS6 3.2 7.0 1.0
CB A:CYS9 3.3 5.3 1.0
CB A:CYS42 3.4 6.8 1.0
HB A:ILE8 3.6 6.5 1.0
HB3 A:TYR11 3.7 7.3 1.0
HB A:ILE41 3.7 8.4 0.7
HB1 A:ALA44 3.8 10.6 1.0
N A:CYS42 3.8 6.7 1.0
HB A:ILE41 3.8 8.7 0.3
N A:CYS9 3.8 5.5 1.0
H A:ALA44 3.9 8.0 1.0
HB2 A:ALA44 4.0 10.6 1.0
CA A:CYS9 4.1 5.2 1.0
HB2 A:CYS9 4.1 6.4 1.0
H A:TYR11 4.1 6.6 1.0
CA A:CYS42 4.1 6.7 1.0
HB2 A:TYR11 4.2 7.3 1.0
HB2 A:CYS42 4.2 8.2 1.0
CB A:ALA44 4.3 7.1 1.0
CB A:TYR11 4.4 6.1 1.0
H A:GLY43 4.5 8.6 1.0
H A:GLY10 4.5 6.7 1.0
H A:ILE41 4.5 8.1 1.0
H A:ILE8 4.6 6.7 1.0
CB A:ILE8 4.6 5.5 1.0
CA A:CYS6 4.6 5.9 1.0
CB A:ILE41 4.6 7.0 0.7
CA A:CYS39 4.7 5.5 1.0
CB A:ILE41 4.7 7.3 0.3
HZ A:PHE49 4.7 9.0 1.0
C A:CYS42 4.7 7.3 1.0
HG23 A:ILE41 4.7 10.7 0.3
N A:ALA44 4.7 6.7 1.0
C A:ILE8 4.8 5.2 1.0
C A:CYS9 4.8 5.2 1.0
N A:GLY43 4.8 7.2 1.0
C A:ILE41 4.8 7.3 1.0
N A:GLY10 4.8 5.6 1.0
N A:TYR11 4.8 5.5 1.0
HA A:CYS9 4.9 6.3 1.0
HG23 A:ILE8 4.9 9.4 1.0
HA A:CYS42 4.9 8.1 1.0
HG21 A:ILE41 4.9 14.4 0.7
HA A:CYS6 5.0 7.0 1.0
HA A:CYS39 5.0 6.6 1.0

Zinc binding site 2 out of 3 in 2pve

Go back to Zinc Binding Sites List in 2pve
Zinc binding site 2 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:5.3
occ:1.00
SG B:CYS142 2.3 5.3 1.0
SG B:CYS109 2.3 6.0 1.0
SG B:CYS106 2.3 5.9 1.0
SG B:CYS139 2.4 4.8 1.0
HB3 B:CYS142 3.1 6.2 1.0
HB3 B:CYS106 3.2 7.4 1.0
HB3 B:CYS139 3.2 5.8 1.0
CB B:CYS106 3.2 6.2 1.0
CB B:CYS139 3.2 4.8 1.0
H B:CYS142 3.2 5.6 1.0
HB2 B:CYS139 3.2 5.8 1.0
H B:CYS109 3.3 8.1 1.0
HB2 B:CYS106 3.3 7.4 1.0
HB3 B:CYS109 3.3 7.7 1.0
CB B:CYS142 3.3 5.2 1.0
CB B:CYS109 3.4 6.4 1.0
HB B:ILE108 3.6 9.5 1.0
HB3 B:TYR111 3.6 8.1 1.0
HB B:ILE141 3.7 6.6 1.0
N B:CYS142 3.8 4.7 1.0
N B:CYS109 3.8 6.7 1.0
HB1 B:ALA144 3.9 9.3 1.0
H B:TYR111 4.0 9.0 1.0
H B:ALA144 4.0 5.9 1.0
HB2 B:ALA144 4.1 9.3 1.0
CA B:CYS142 4.1 4.9 1.0
HB2 B:CYS142 4.1 6.2 1.0
HB2 B:TYR111 4.1 8.1 1.0
CA B:CYS109 4.1 6.9 1.0
HB2 B:CYS109 4.2 7.7 1.0
CB B:TYR111 4.3 6.7 1.0
CB B:ALA144 4.4 6.2 1.0
H B:GLY110 4.5 8.9 1.0
HZ B:PHE149 4.5 7.4 1.0
CB B:ILE108 4.5 7.9 1.0
H B:ILE141 4.5 5.4 1.0
H B:ILE108 4.6 9.0 1.0
CB B:ILE141 4.6 5.5 1.0
H B:GLY143 4.6 5.5 1.0
CA B:CYS139 4.6 4.4 1.0
CA B:CYS106 4.7 6.2 1.0
HG23 B:ILE108 4.7 13.3 1.0
C B:CYS142 4.7 4.5 1.0
C B:CYS109 4.7 7.0 1.0
N B:TYR111 4.8 7.5 1.0
HG21 B:ILE141 4.8 10.8 1.0
C B:ILE108 4.8 7.8 1.0
N B:GLY110 4.8 7.5 1.0
N B:ALA144 4.8 4.9 1.0
C B:ILE141 4.9 4.5 1.0
N B:GLY143 4.9 4.6 1.0
HA B:CYS142 4.9 5.8 1.0
HA B:CYS109 5.0 8.3 1.0
CZ B:PHE149 5.0 6.2 1.0
HA B:CYS139 5.0 5.3 1.0
HA B:CYS106 5.0 7.4 1.0

Zinc binding site 3 out of 3 in 2pve

Go back to Zinc Binding Sites List in 2pve
Zinc binding site 3 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:5.4
occ:1.00
SG C:CYS209 2.3 5.7 1.0
SG C:CYS242 2.3 5.9 1.0
SG C:CYS206 2.3 5.2 1.0
SG C:CYS239 2.4 5.5 1.0
HB3 C:CYS209 3.1 6.7 1.0
HB3 C:CYS206 3.1 6.4 1.0
CB C:CYS206 3.1 5.3 1.0
CB C:CYS239 3.2 5.2 1.0
HB3 C:CYS239 3.2 6.2 1.0
HB2 C:CYS239 3.2 6.2 1.0
HB2 C:CYS206 3.2 6.4 1.0
H C:CYS242 3.2 7.7 1.0
H C:CYS209 3.2 6.2 1.0
HB3 C:CYS242 3.2 8.1 1.0
CB C:CYS209 3.3 5.6 1.0
CB C:CYS242 3.4 6.8 1.0
HB3 C:TYR211 3.6 8.4 1.0
HB C:ILE241 3.7 8.7 1.0
HB1 C:ALA244 3.7 9.7 1.0
HB C:ILE208 3.8 6.3 1.0
N C:CYS209 3.8 5.2 1.0
N C:CYS242 3.8 6.4 1.0
H C:ALA244 4.0 7.0 1.0
H C:TYR211 4.0 7.8 1.0
HB2 C:ALA244 4.0 9.7 1.0
HB2 C:CYS209 4.0 6.7 1.0
CA C:CYS209 4.0 5.4 1.0
HB2 C:TYR211 4.0 8.4 1.0
CA C:CYS242 4.1 6.9 1.0
HB2 C:CYS242 4.2 8.1 1.0
CB C:TYR211 4.3 7.0 1.0
CB C:ALA244 4.3 6.5 1.0
H C:GLY210 4.4 7.2 1.0
H C:GLY243 4.5 7.2 1.0
HZ C:PHE249 4.5 7.8 1.0
H C:ILE241 4.5 8.6 1.0
CA C:CYS206 4.6 4.7 1.0
CB C:ILE241 4.6 7.2 1.0
CA C:CYS239 4.6 5.3 1.0
H C:ILE208 4.6 6.2 1.0
CB C:ILE208 4.7 5.3 1.0
C C:CYS209 4.7 5.3 1.0
N C:ALA244 4.7 5.8 1.0
C C:CYS242 4.7 6.2 1.0
N C:TYR211 4.8 6.5 1.0
N C:GLY210 4.8 6.0 1.0
N C:GLY243 4.8 6.0 1.0
C C:ILE208 4.8 5.5 1.0
C C:ILE241 4.9 7.2 1.0
HA C:CYS209 4.9 6.4 1.0
HG23 C:ILE208 4.9 9.3 1.0
HA C:CYS206 4.9 5.6 1.0
HA C:CYS242 4.9 8.3 1.0
HA C:CYS239 4.9 6.3 1.0
HG21 C:ILE241 5.0 12.6 1.0

Reference:

D.M.Lemaster, J.S.Anderson, L.Wang, Y.Guo, H.Li, G.Hernandez. uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin. Bmc Struct.Biol. V. 7 81 2007.
ISSN: ESSN 1472-6807
PubMed: 18053245
DOI: 10.1186/1472-6807-7-81
Page generated: Wed Dec 16 03:49:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy