Atomistry » Iron » PDB 6vk8-6wnb » 6vzy
Atomistry »
  Iron »
    PDB 6vk8-6wnb »
      6vzy »

Iron in PDB 6vzy: Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor

Protein crystallography data

The structure of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy was solved by M.J.Mcbride, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.42 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.953, 105.848, 150.591, 90, 90, 90
R / Rfree (%) 19 / 22.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor (pdb code 6vzy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 1 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.2
occ:0.93
OE2 A:GLU215 2.1 19.0 1.0
ND1 A:HIS225 2.1 10.0 1.0
NE2 A:HIS311 2.1 10.4 1.0
O A:HOH743 2.2 19.8 1.0
OE2 A:GLU189 2.2 21.3 1.0
OE1 A:GLU189 2.2 14.4 1.0
CD A:GLU189 2.5 19.6 1.0
CE1 A:HIS225 2.9 17.2 1.0
CE1 A:HIS311 3.0 16.8 1.0
CD2 A:HIS311 3.1 18.4 1.0
CD A:GLU215 3.2 19.9 1.0
CG A:HIS225 3.2 11.7 1.0
CB A:HIS225 3.7 15.2 1.0
CG A:GLU189 4.0 19.1 1.0
O A:HOH667 4.0 20.1 1.0
OE1 A:GLU215 4.0 19.5 1.0
CG A:GLU215 4.0 13.3 1.0
CB A:GLU215 4.0 12.3 1.0
O A:HOH760 4.0 26.2 1.0
NE2 A:HIS225 4.1 14.8 1.0
ND1 A:HIS311 4.2 12.4 1.0
CA A:GLU215 4.2 10.8 1.0
CG A:HIS311 4.2 15.7 1.0
CD2 A:HIS225 4.3 16.2 1.0
OH A:TYR307 4.5 13.1 1.0
O A:GLU215 4.8 12.8 1.0
CB A:GLU189 5.0 12.9 1.0
CE2 A:TYR307 5.0 10.2 1.0

Iron binding site 2 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 2 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:11.4
occ:0.67
OE1 A:GLU281 2.0 22.9 1.0
OD1 A:ASP315 2.0 26.4 1.0
OE1 A:GLU215 2.0 19.5 1.0
ND1 A:HIS318 2.1 13.9 1.0
O A:HOH667 2.1 20.1 1.0
CE1 A:HIS318 2.9 18.8 1.0
CD A:GLU281 3.1 25.9 1.0
CG A:ASP315 3.1 33.2 1.0
CD A:GLU215 3.2 19.9 1.0
CG A:HIS318 3.2 18.2 1.0
OE2 A:GLU281 3.4 22.8 1.0
OD2 A:ASP315 3.5 22.5 1.0
OE2 A:GLU215 3.6 19.0 1.0
CB A:HIS318 3.7 19.8 1.0
NE2 A:HIS318 4.1 20.6 1.0
CD2 A:HIS318 4.3 23.2 1.0
CG1 A:VAL211 4.3 15.4 1.0
CG A:GLU281 4.4 18.7 1.0
CB A:ASP315 4.4 17.9 1.0
CG A:GLU215 4.5 13.3 1.0
O A:HOH743 4.5 19.8 1.0
CA A:ASP315 4.7 22.3 1.0
CD2 A:HIS311 4.7 18.4 1.0
CG2 A:ILE314 4.9 34.0 1.0
CB A:GLU281 5.0 19.6 1.0

Iron binding site 3 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 3 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:16.0
occ:1.00
NE2 A:HIS409 2.2 13.2 1.0
NE2 A:HIS407 2.2 11.3 1.0
NE2 A:HIS448 2.2 10.7 1.0
O A:HOH780 2.3 20.1 1.0
CE1 A:HIS409 3.1 11.1 1.0
CD2 A:HIS407 3.1 16.3 1.0
CE1 A:HIS407 3.2 15.4 1.0
CE1 A:HIS448 3.2 14.6 1.0
CD2 A:HIS448 3.2 10.1 1.0
CD2 A:HIS409 3.2 11.1 1.0
O A:HOH771 4.0 27.4 1.0
OE2 A:GLU413 4.2 26.7 1.0
ND1 A:HIS409 4.3 16.6 1.0
ND1 A:HIS407 4.3 9.8 1.0
CG A:HIS407 4.3 10.2 1.0
ND1 A:HIS448 4.3 10.8 1.0
CG A:HIS409 4.3 12.4 1.0
CG A:HIS448 4.3 8.3 1.0
O A:HOH782 4.6 29.4 1.0
CD1 A:ILE442 4.9 16.9 1.0

Iron binding site 4 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 4 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.2
occ:1.00
O B:HOH719 2.1 16.3 1.0
OE2 B:GLU189 2.1 16.6 1.0
NE2 B:HIS311 2.1 11.9 1.0
ND1 B:HIS225 2.1 10.7 1.0
OE2 B:GLU215 2.2 14.4 1.0
OE1 B:GLU189 2.3 15.9 1.0
CD B:GLU189 2.5 16.7 1.0
CE1 B:HIS225 2.9 12.0 1.0
CE1 B:HIS311 3.0 14.1 1.0
CD2 B:HIS311 3.1 17.3 1.0
CG B:HIS225 3.2 9.0 1.0
CD B:GLU215 3.3 18.7 1.0
CB B:HIS225 3.7 10.0 1.0
CG B:GLU189 3.9 13.4 1.0
CB B:GLU215 4.0 13.4 1.0
O B:HOH677 4.0 17.8 1.0
CG B:GLU215 4.1 12.5 1.0
NE2 B:HIS225 4.1 15.7 1.0
OE1 B:GLU215 4.1 17.6 1.0
ND1 B:HIS311 4.1 14.1 1.0
CG B:HIS311 4.2 12.1 1.0
O B:HOH777 4.2 21.8 1.0
CD2 B:HIS225 4.3 13.3 1.0
CA B:GLU215 4.3 12.7 1.0
O B:HOH793 4.3 24.4 1.0
OH B:TYR307 4.5 12.1 1.0
O B:GLU215 4.8 12.2 1.0
CE1 B:TYR307 4.9 12.5 1.0
CB B:GLU189 5.0 10.7 1.0
FE B:FE2502 5.0 14.6 0.8

Iron binding site 5 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 5 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:14.6
occ:0.84
OE1 B:GLU281 2.0 20.1 1.0
OD1 B:ASP315 2.0 22.2 1.0
OE1 B:GLU215 2.1 17.6 1.0
O B:HOH677 2.1 17.8 1.0
ND1 B:HIS318 2.2 17.2 1.0
CD B:GLU281 3.0 22.0 1.0
CE1 B:HIS318 3.1 21.9 1.0
CG B:ASP315 3.1 22.9 1.0
CD B:GLU215 3.2 18.7 1.0
CG B:HIS318 3.3 20.8 1.0
OE2 B:GLU281 3.4 21.2 1.0
OE2 B:GLU215 3.5 14.4 1.0
OD2 B:ASP315 3.6 23.4 1.0
CB B:HIS318 3.7 16.3 1.0
NE2 B:HIS318 4.3 26.3 1.0
CG1 B:VAL211 4.3 15.7 1.0
CG B:GLU281 4.3 19.7 1.0
CD2 B:HIS318 4.4 22.5 1.0
O B:HOH719 4.4 16.3 1.0
CB B:ASP315 4.4 18.3 1.0
CG B:GLU215 4.5 12.5 1.0
CA B:ASP315 4.6 19.7 1.0
CD2 B:HIS311 4.7 17.3 1.0
CG2 B:ILE314 4.8 29.3 1.0
CB B:GLU281 4.9 15.9 1.0
FE B:FE2501 5.0 13.2 1.0

Iron binding site 6 out of 6 in 6vzy

Go back to Iron Binding Sites List in 6vzy
Iron binding site 6 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe503

b:17.4
occ:0.97
NE2 B:HIS409 2.2 16.3 1.0
NE2 B:HIS407 2.2 11.2 1.0
NE2 B:HIS448 2.2 11.7 1.0
O B:HOH789 2.3 18.6 1.0
CD2 B:HIS409 3.1 16.1 1.0
CE1 B:HIS407 3.1 18.8 1.0
CD2 B:HIS448 3.2 12.6 1.0
CD2 B:HIS407 3.2 13.4 1.0
CE1 B:HIS448 3.2 9.0 1.0
CE1 B:HIS409 3.2 9.6 1.0
OE2 B:GLU413 4.2 23.6 1.0
ND1 B:HIS407 4.3 12.7 1.0
CG B:HIS409 4.3 14.4 1.0
ND1 B:HIS448 4.3 9.1 1.0
CG B:HIS448 4.3 11.0 1.0
ND1 B:HIS409 4.3 16.8 1.0
CG B:HIS407 4.3 9.4 1.0
O B:HOH796 4.4 24.5 1.0
CD1 B:ILE442 4.7 13.9 1.0

Reference:

M.J.Mcbride, S.R.Pope, K.Hu, C.D.Okafor, E.P.Balskus, J.M.Bollinger Jr., A.K.Boal. Structure and Assembly of the Diiron Cofactor in the Heme-Oxygenase-Like Domain of the N-Nitrosourea-Producing Enzyme Sznf Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
Page generated: Wed Aug 7 13:46:19 2024

Last articles

Cl in 3TGO
Cl in 3TFS
Cl in 3TG8
Cl in 3TFR
Cl in 3TFP
Cl in 3TFC
Cl in 3TCT
Cl in 3TF6
Cl in 3TDX
Cl in 3TEE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy