Iron in PDB 1qyb: X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures

The structure of X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures, PDB code: 1qyb was solved by S.Jin, D.M.Kurtz, Z.J.Liu, J.Rose, B.C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.59 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.008, 80.161, 101.029, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.3

The structure of X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures (pdb code 1qyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures, PDB code: 1qyb:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:24.1 occ:0.51 OE1 A:GLU128 2.2 20.2 1.0 OE2 A:GLU53 2.2 24.1 1.0 OE2 A:GLU94 2.2 20.2 1.0 O A:HOH1079 2.2 26.5 1.0 ND1 A:HIS131 2.3 12.5 1.0 OE1 A:GLU94 2.3 20.3 1.0 CD A:GLU94 2.6 20.5 1.0 CD A:GLU128 3.0 19.1 1.0 CD A:GLU53 3.2 19.7 1.0 CE1 A:HIS131 3.2 12.6 1.0 CG A:HIS131 3.3 12.4 1.0 FE A:FE601 3.4 30.8 0.3 OE2 A:GLU128 3.5 24.6 1.0 FE A:FE601 3.6 30.8 0.2 OE1 A:GLU53 3.6 25.4 1.0 CB A:HIS131 3.7 11.8 1.0 CA A:GLU128 4.1 11.4 1.0 CG A:GLU94 4.1 18.6 1.0 CG A:GLU128 4.2 14.7 1.0 CB A:GLU128 4.3 14.4 1.0 NE2 A:HIS131 4.4 13.4 1.0 CG A:GLU53 4.4 16.2 1.0 CG2 A:THR49 4.4 8.8 1.0 CD2 A:HIS131 4.4 13.0 1.0 CE2 A:TYR27 4.5 12.6 1.0 CE1 A:HIS56 4.5 14.5 1.0 OH A:TYR27 4.5 14.8 1.0 ND1 A:HIS56 4.8 15.2 1.0 OE1 A:GLU97 4.9 31.1 1.0 O A:GLU128 4.9 13.6 1.0 N A:GLU128 4.9 13.0 1.0 CB A:GLU94 5.0 16.3 1.0

Iron binding site 2 out of 3 in the X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:30.8 occ:0.34 FE A:FE601 0.0 30.8 0.3 FE A:FE601 1.9 30.8 0.2 OE2 A:GLU128 2.0 24.6 1.0 O A:HOH1079 2.0 26.5 1.0 OE1 A:GLU20 2.0 26.1 1.0 OE1 A:GLU53 2.2 25.4 1.0 OE1 A:GLU97 2.3 31.1 1.0 OE2 A:GLU20 2.6 22.2 1.0 CD A:GLU20 2.6 22.1 1.0 CD A:GLU128 2.9 19.1 1.0 CD A:GLU53 3.1 19.7 1.0 OE2 A:GLU53 3.2 24.1 1.0 OE1 A:GLU128 3.3 20.2 1.0 CD A:GLU97 3.3 31.4 1.0 FE A:FE600 3.4 24.1 0.5 OE2 A:GLU97 3.6 34.7 1.0 O A:HOH1138 3.9 42.2 1.0 ND1 A:HIS56 4.0 15.2 1.0 CG A:GLU20 4.1 17.2 1.0 CG A:GLU128 4.2 14.7 1.0 CG A:GLU53 4.5 16.2 1.0 OH A:TYR102 4.5 23.9 1.0 OE1 A:GLU94 4.5 20.3 1.0 CE1 A:HIS56 4.6 14.5 1.0 CG A:GLU97 4.7 27.6 1.0 CE2 A:TYR102 4.7 20.2 1.0 OE2 A:GLU94 4.7 20.2 1.0 CB A:GLU20 4.8 13.7 1.0 CA A:GLU20 4.8 12.0 1.0 CD A:GLU94 5.0 20.5 1.0 CB A:ALA23 5.0 10.6 1.0

Iron binding site 3 out of 3 in the X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)4] Site and Alternative Diiron Site Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:30.8 occ:0.23 FE A:FE601 0.0 30.8 0.2 FE A:FE601 1.9 30.8 0.3 OE2 A:GLU20 2.1 22.2 1.0 ND1 A:HIS56 2.1 15.2 1.0 OE2 A:GLU128 2.2 24.6 1.0 OE1 A:GLU53 2.4 25.4 1.0 OE2 A:GLU53 2.7 24.1 1.0 CD A:GLU20 2.8 22.1 1.0 CD A:GLU53 2.8 19.7 1.0 CD A:GLU128 2.9 19.1 1.0 OE1 A:GLU20 2.9 26.1 1.0 CE1 A:HIS56 2.9 14.5 1.0 OE1 A:GLU128 2.9 20.2 1.0 O A:HOH1079 3.3 26.5 1.0 CG A:HIS56 3.3 13.7 1.0 FE A:FE600 3.6 24.1 0.5 CB A:HIS56 3.8 11.7 1.0 OE1 A:GLU97 4.0 31.1 1.0 CG A:GLU20 4.1 17.2 1.0 CG A:GLU53 4.1 16.2 1.0 NE2 A:HIS56 4.1 14.2 1.0 CA A:GLU53 4.2 9.9 1.0 CG A:GLU128 4.3 14.7 1.0 CD2 A:HIS56 4.3 14.8 1.0 CB A:GLU53 4.4 11.5 1.0 CG2 A:ILE124 4.5 14.5 1.0 OH A:TYR102 4.5 23.9 1.0 CB A:GLU20 4.8 13.7 1.0 ND1 A:HIS131 4.9 12.5 1.0 CE1 A:HIS131 4.9 12.6 1.0

S.Jin, D.M.Kurtz, Z.J.Liu, J.Rose, B.C.Wang. X-Ray Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin with Zinc Substituted Into the [Fe(Scys)(4)] Site and Alternative Diiron Site Structures. Biochemistry V. 43 3204 2004.
ISSN: ISSN 0006-2960
PubMed: 15023070
DOI: 10.1021/BI0356193