Atomistry » Zinc » PDB 2vh5-2vqw » 2vkr
Atomistry »
  Zinc »
    PDB 2vh5-2vqw »
      2vkr »

Zinc in PDB 2vkr: 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin

Protein crystallography data

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr was solved by C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.48 / 2.01
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 117.500, 117.500, 50.900, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 27.3

Other elements in 2vkr:

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin also contains other interesting chemical elements:

Iron (Fe) 49 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin (pdb code 2vkr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 1 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn106

b:0.2
occ:1.00
 NE2 A:HIS19 1.8 24.6 1.0
ND1 A:HIS16 1.8 26.2 1.0
OD1 A:ASP76 1.8 17.5 1.0
ND1 A:HIS34 1.9 19.7 1.0
CE1 A:HIS19 2.6 27.1 1.0
CE1 A:HIS16 2.7 30.0 1.0
CE1 A:HIS34 2.7 18.0 1.0
CG A:ASP76 2.7 28.0 1.0
CG A:HIS16 2.9 30.4 1.0
CD2 A:HIS19 2.9 26.8 1.0
OD2 A:ASP76 3.0 24.9 1.0
CG A:HIS34 3.0 21.2 1.0
CB A:HIS16 3.4 31.7 1.0
CB A:HIS34 3.6 22.7 1.0
ND1 A:HIS19 3.8 25.4 1.0
NE2 A:HIS16 3.8 29.1 1.0
NE2 A:HIS34 3.9 20.0 1.0
CD2 A:HIS16 4.0 29.9 1.0
CG A:HIS19 4.0 26.3 1.0
CD2 A:HIS34 4.1 20.0 1.0
O A:HIS16 4.1 29.4 1.0
CB A:ASP76 4.1 21.0 1.0
CZ A:PHE42 4.3 19.4 1.0
CE2 A:PHE42 4.5 22.1 1.0
C A:HIS16 4.6 30.0 1.0
CD A:PRO77 4.6 20.8 1.0
CA A:HIS16 4.6 30.7 1.0
CA A:HIS34 4.8 24.2 1.0
CA A:ASP76 4.9 22.3 1.0

Zinc binding site 2 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 2 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn106

b:0.5
occ:1.00
 NE2 B:HIS19 1.8 24.6 1.0
OD1 B:ASP76 1.8 17.5 1.0
ND1 B:HIS16 1.8 26.1 1.0
ND1 B:HIS34 1.9 19.7 1.0
CE1 B:HIS19 2.6 27.1 1.0
CE1 B:HIS16 2.6 29.9 1.0
CE1 B:HIS34 2.7 18.0 1.0
CG B:ASP76 2.8 28.0 1.0
CG B:HIS16 2.9 30.4 1.0
CD2 B:HIS19 3.0 26.8 1.0
CG B:HIS34 3.0 21.2 1.0
OD2 B:ASP76 3.1 24.8 1.0
CB B:HIS16 3.5 31.7 1.0
CB B:HIS34 3.6 22.7 1.0
ND1 B:HIS19 3.8 25.4 1.0
NE2 B:HIS16 3.8 29.1 1.0
NE2 B:HIS34 3.9 19.9 1.0
CD2 B:HIS16 4.0 29.9 1.0
CG B:HIS19 4.0 26.3 1.0
CD2 B:HIS34 4.1 20.0 1.0
CB B:ASP76 4.1 21.0 1.0
O B:HIS16 4.2 29.4 1.0
CZ B:PHE42 4.3 19.5 1.0
CE2 B:PHE42 4.6 22.1 1.0
CD B:PRO77 4.7 20.9 1.0
CA B:HIS16 4.7 30.7 1.0
C B:HIS16 4.7 30.0 1.0
CA B:ASP76 4.9 22.4 1.0
CA B:HIS34 4.9 24.2 1.0
CG2 B:VAL21 4.9 27.1 1.0

Zinc binding site 3 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 3 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn106

b:3.3
occ:1.00
 NE2 C:HIS19 1.8 24.5 1.0
ND1 C:HIS16 1.8 26.2 1.0
OD1 C:ASP76 1.8 17.6 1.0
ND1 C:HIS34 1.9 19.7 1.0
CE1 C:HIS19 2.6 27.0 1.0
CE1 C:HIS16 2.7 30.0 1.0
CE1 C:HIS34 2.7 17.9 1.0
CG C:ASP76 2.7 28.0 1.0
CD2 C:HIS19 2.9 26.8 1.0
CG C:HIS16 2.9 30.4 1.0
OD2 C:ASP76 3.0 24.9 1.0
CG C:HIS34 3.0 21.1 1.0
CB C:HIS16 3.5 31.7 1.0
CB C:HIS34 3.6 22.7 1.0
ND1 C:HIS19 3.8 25.4 1.0
NE2 C:HIS16 3.8 29.1 1.0
NE2 C:HIS34 3.9 20.0 1.0
CG C:HIS19 4.0 26.3 1.0
CD2 C:HIS16 4.0 30.0 1.0
CD2 C:HIS34 4.1 20.0 1.0
CZ C:PHE42 4.1 19.5 1.0
CB C:ASP76 4.1 21.0 1.0
O C:HIS16 4.3 29.3 1.0
CD C:PRO77 4.5 20.8 1.0
CE2 C:PHE42 4.5 22.1 1.0
C C:HIS16 4.7 30.0 1.0
CA C:HIS16 4.7 30.7 1.0
CA C:ASP76 4.8 22.3 1.0
CA C:HIS34 4.9 24.2 1.0

Zinc binding site 4 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 4 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn106

b:0.5
occ:1.00
 NE2 D:HIS19 1.8 24.6 1.0
ND1 D:HIS16 1.8 26.0 1.0
OD1 D:ASP76 1.8 17.4 1.0
ND1 D:HIS34 1.9 19.8 1.0
CE1 D:HIS19 2.6 27.1 1.0
CE1 D:HIS16 2.7 30.0 1.0
CE1 D:HIS34 2.7 18.0 1.0
CG D:ASP76 2.7 28.1 1.0
CG D:HIS16 2.9 30.4 1.0
CD2 D:HIS19 3.0 26.8 1.0
OD2 D:ASP76 3.0 24.9 1.0
CG D:HIS34 3.0 21.2 1.0
CB D:HIS16 3.5 31.7 1.0
CB D:HIS34 3.5 22.7 1.0
ND1 D:HIS19 3.8 25.4 1.0
NE2 D:HIS16 3.8 29.1 1.0
NE2 D:HIS34 3.9 20.0 1.0
CD2 D:HIS16 4.0 30.0 1.0
CG D:HIS19 4.0 26.3 1.0
CD2 D:HIS34 4.1 20.0 1.0
CB D:ASP76 4.2 21.0 1.0
O D:HIS16 4.2 29.4 1.0
CZ D:PHE42 4.3 19.4 1.0
CD D:PRO77 4.5 20.8 1.0
CE2 D:PHE42 4.6 22.1 1.0
C D:HIS16 4.7 30.0 1.0
CA D:HIS16 4.7 30.7 1.0
CG2 D:VAL21 4.7 27.1 1.0
CA D:HIS34 4.8 24.3 1.0
CA D:ASP76 4.9 22.3 1.0

Zinc binding site 5 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 5 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn106

b:24.1
occ:1.00
 NE2 E:HIS19 1.8 24.7 1.0
OD1 E:ASP76 1.8 45.4 1.0
ND1 E:HIS16 1.8 26.3 1.0
ND1 E:HIS34 1.9 19.8 1.0
CE1 E:HIS19 2.6 27.2 1.0
CE1 E:HIS16 2.7 30.1 1.0
CE1 E:HIS34 2.7 18.0 1.0
CG E:ASP76 2.7 55.2 1.0
CG E:HIS16 2.9 30.4 1.0
CD2 E:HIS19 2.9 26.9 1.0
OD2 E:ASP76 3.0 65.0 1.0
CG E:HIS34 3.0 21.2 1.0
CB E:HIS34 3.5 22.7 1.0
CB E:HIS16 3.5 31.8 1.0
ND1 E:HIS19 3.8 25.4 1.0
NE2 E:HIS16 3.8 29.3 1.0
NE2 E:HIS34 3.9 20.0 1.0
CG E:HIS19 4.0 26.4 1.0
CD2 E:HIS16 4.0 29.9 1.0
O E:HIS16 4.0 29.5 1.0
CD2 E:HIS34 4.1 20.0 1.0
CB E:ASP76 4.1 48.7 1.0
CE2 E:PHE42 4.2 22.1 1.0
CZ E:PHE42 4.2 19.4 1.0
CD E:PRO77 4.4 48.4 1.0
C E:HIS16 4.5 30.1 1.0
CA E:HIS16 4.6 30.7 1.0
CA E:HIS34 4.7 24.3 1.0
NE2 E:GLN17 4.7 55.4 1.0
CA E:ASP76 5.0 46.4 1.0

Zinc binding site 6 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 6 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn106

b:8.1
occ:1.00
 NE2 F:HIS19 1.8 24.6 1.0
OD1 F:ASP76 1.8 17.5 1.0
ND1 F:HIS16 1.8 26.2 1.0
ND1 F:HIS34 1.9 19.7 1.0
CE1 F:HIS19 2.6 27.1 1.0
CE1 F:HIS16 2.6 30.0 1.0
CE1 F:HIS34 2.7 18.1 1.0
CG F:ASP76 2.8 28.0 1.0
CD2 F:HIS19 2.9 26.8 1.0
CG F:HIS16 3.0 30.4 1.0
OD2 F:ASP76 3.0 24.9 1.0
CG F:HIS34 3.0 21.2 1.0
CB F:HIS16 3.5 31.7 1.0
CB F:HIS34 3.6 22.8 1.0
ND1 F:HIS19 3.8 25.4 1.0
NE2 F:HIS16 3.8 29.1 1.0
NE2 F:HIS34 3.9 20.1 1.0
CD2 F:HIS16 4.0 29.9 1.0
CG F:HIS19 4.0 26.3 1.0
CD2 F:HIS34 4.1 20.0 1.0
CB F:ASP76 4.1 21.0 1.0
O F:HIS16 4.2 29.5 1.0
CZ F:PHE42 4.3 19.4 1.0
CD F:PRO77 4.4 20.8 1.0
CE2 F:PHE42 4.6 22.1 1.0
C F:HIS16 4.6 30.1 1.0
CA F:HIS16 4.7 30.7 1.0
CG2 F:VAL21 4.7 27.2 1.0
CA F:ASP76 4.8 22.4 1.0
CA F:HIS34 4.9 24.3 1.0

Zinc binding site 7 out of 7 in 2vkr

Go back to Zinc Binding Sites List in 2vkr
Zinc binding site 7 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn106

b:5.1
occ:1.00
 NE2 G:HIS19 1.8 24.6 1.0
OD1 G:ASP76 1.8 17.5 1.0
ND1 G:HIS16 1.8 26.2 1.0
ND1 G:HIS34 1.9 19.8 1.0
CE1 G:HIS19 2.6 27.1 1.0
CE1 G:HIS16 2.7 30.1 1.0
CE1 G:HIS34 2.7 18.0 1.0
CG G:ASP76 2.8 28.0 1.0
CG G:HIS16 2.9 30.4 1.0
CD2 G:HIS19 2.9 26.9 1.0
CG G:HIS34 3.1 21.2 1.0
OD2 G:ASP76 3.1 24.9 1.0
CB G:HIS16 3.4 31.7 1.0
CB G:HIS34 3.6 22.6 1.0
ND1 G:HIS19 3.8 25.4 1.0
NE2 G:HIS16 3.8 29.1 1.0
NE2 G:HIS34 3.9 20.0 1.0
CD2 G:HIS16 4.0 29.9 1.0
CG G:HIS19 4.0 26.4 1.0
CD2 G:HIS34 4.1 20.0 1.0
CB G:ASP76 4.1 21.0 1.0
O G:HIS16 4.2 29.4 1.0
CZ G:PHE42 4.4 19.4 1.0
CD G:PRO77 4.4 20.8 1.0
C G:HIS16 4.6 30.1 1.0
CA G:HIS16 4.6 30.7 1.0
CE2 G:PHE42 4.8 22.1 1.0
CA G:ASP76 4.8 22.3 1.0
CA G:HIS34 4.8 24.3 1.0

Reference:

C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo. Crystallographic Analysis of the Intact Metal Centres [3FE-4S](1+/0) and [4FE-4S](2+/1+) in A Zn(2+) -Containing Ferredoxin. Febs Lett. V. 582 763 2008.
ISSN: ISSN 0014-5793
PubMed: 18258200
DOI: 10.1016/J.FEBSLET.2008.01.041
Page generated: Thu Oct 17 04:20:27 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy