Iron in PDB 2vsf: Structure of Xpd From Thermoplasma Acidophilum

The structure of Structure of Xpd From Thermoplasma Acidophilum, PDB code: 2vsf was solved by J.Kuper, S.C.Wolski, J.J.Truglio, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.9
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	78.890, 78.890, 174.040, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 28.7

The structure of Structure of Xpd From Thermoplasma Acidophilum also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Structure of Xpd From Thermoplasma Acidophilum (pdb code 2vsf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Xpd From Thermoplasma Acidophilum, PDB code: 2vsf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Xpd From Thermoplasma Acidophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Xpd From Thermoplasma Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:61.9 occ:1.00 FE1 A:SF41616 0.0 61.9 1.0 S4 A:SF41616 2.3 64.6 1.0 S3 A:SF41616 2.3 60.2 1.0 S2 A:SF41616 2.3 68.0 1.0 SG A:CYS92 2.4 67.2 1.0 FE3 A:SF41616 2.7 67.1 1.0 FE2 A:SF41616 2.7 60.1 1.0 FE4 A:SF41616 2.7 59.5 1.0 CB A:CYS92 3.5 64.1 1.0 CA A:CYS92 3.9 63.5 1.0 S1 A:SF41616 3.9 60.2 1.0 CB A:LEU94 4.0 63.2 1.0 N A:LEU94 4.1 63.5 1.0 N A:ILE93 4.2 63.1 1.0 C A:CYS92 4.4 62.9 1.0 SG A:CYS113 4.6 60.9 1.0 CE2 A:PHE112 4.6 62.1 1.0 CA A:LEU94 4.7 63.8 1.0 CB A:CYS113 4.8 60.0 1.0 SG A:CYS164 4.8 61.8 1.0 N A:TYR95 4.9 66.0 1.0 SG A:CYS128 5.0 56.2 1.0

Iron binding site 2 out of 4 in the Structure of Xpd From Thermoplasma Acidophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Xpd From Thermoplasma Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:60.1 occ:1.00 FE2 A:SF41616 0.0 60.1 1.0 S3 A:SF41616 2.3 60.2 1.0 S1 A:SF41616 2.3 60.2 1.0 S4 A:SF41616 2.3 64.6 1.0 SG A:CYS128 2.5 56.2 1.0 FE4 A:SF41616 2.7 59.5 1.0 FE3 A:SF41616 2.7 67.1 1.0 FE1 A:SF41616 2.7 61.9 1.0 CB A:CYS128 3.7 56.3 1.0 S2 A:SF41616 3.9 68.0 1.0 CB A:LEU94 4.2 63.2 1.0 CD2 A:LEU94 4.5 64.7 1.0 CB A:TYR130 4.6 57.0 1.0 SG A:CYS164 4.7 61.8 1.0 CB A:CYS164 4.7 60.7 1.0 SG A:CYS113 4.8 60.9 1.0 CB A:PHE131 4.9 58.5 1.0 CG A:LEU94 4.9 62.9 1.0 SG A:CYS92 5.0 67.2 1.0

Iron binding site 3 out of 4 in the Structure of Xpd From Thermoplasma Acidophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Xpd From Thermoplasma Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:67.1 occ:1.00 FE3 A:SF41616 0.0 67.1 1.0 S2 A:SF41616 2.3 68.0 1.0 S4 A:SF41616 2.3 64.6 1.0 S1 A:SF41616 2.3 60.2 1.0 SG A:CYS113 2.3 60.9 1.0 FE4 A:SF41616 2.7 59.5 1.0 FE2 A:SF41616 2.7 60.1 1.0 FE1 A:SF41616 2.7 61.9 1.0 CB A:CYS113 3.4 60.0 1.0 S3 A:SF41616 3.9 60.2 1.0 NE A:ARG88 4.1 60.0 1.0 CA A:CYS113 4.2 60.0 1.0 CD A:LYS117 4.4 65.9 1.0 SG A:CYS164 4.5 61.8 1.0 CG A:GLU167 4.6 60.6 1.0 SG A:CYS92 4.7 67.2 1.0 O A:CYS113 4.8 61.8 1.0 CG A:LYS117 4.8 64.1 1.0 C A:CYS113 4.8 60.2 1.0 NH2 A:ARG88 4.8 62.8 1.0 CD A:ARG88 4.8 62.5 1.0 SG A:CYS128 5.0 56.2 1.0 CZ A:ARG88 5.0 59.6 1.0

Iron binding site 4 out of 4 in the Structure of Xpd From Thermoplasma Acidophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Xpd From Thermoplasma Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:59.5 occ:1.00 FE4 A:SF41616 0.0 59.5 1.0 SG A:CYS164 2.2 61.8 1.0 S1 A:SF41616 2.3 60.2 1.0 S3 A:SF41616 2.3 60.2 1.0 S2 A:SF41616 2.3 68.0 1.0 FE2 A:SF41616 2.7 60.1 1.0 FE3 A:SF41616 2.7 67.1 1.0 FE1 A:SF41616 2.7 61.9 1.0 CB A:CYS164 3.0 60.7 1.0 S4 A:SF41616 3.9 64.6 1.0 CA A:CYS164 4.2 60.5 1.0 CG A:GLU167 4.5 60.6 1.0 CA A:CYS92 4.6 63.5 1.0 SG A:CYS92 4.7 67.2 1.0 SG A:CYS128 4.8 56.2 1.0 N A:ILE93 4.8 63.1 1.0 CB A:TYR130 4.9 57.0 1.0 SG A:CYS113 4.9 60.9 1.0 C A:CYS164 4.9 60.9 1.0 CB A:CYS92 4.9 64.1 1.0

S.C.Wolski, J.Kuper, P.Haenzelmann, J.J.Truglio, D.L.Croteau, B.Van Houten, C.Kisker. Crystal Structure of the Fes Cluster-Containing Nucleotide Excision Repair Helicase Xpd. Plos Biol. V. 6 E149 2008.
ISSN: ISSN 1544-9173
PubMed: 18578568
DOI: 10.1371/JOURNAL.PBIO.0060149