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Iron in PDB 3aqj: Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv

Protein crystallography data

The structure of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv, PDB code: 3aqj was solved by S.Takeda, E.Yamashita, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.42 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.912, 64.463, 67.186, 90.00, 91.32, 90.00
R / Rfree (%) 16 / 19

Other elements in 3aqj:

The structure of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv (pdb code 3aqj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv, PDB code: 3aqj:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3aqj

Go back to Iron Binding Sites List in 3aqj
Iron binding site 1 out of 2 in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv


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 A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe135

b:5.5
occ:1.00
NE2 A:HIS120 2.2 5.7 1.0
NE2 C:HIS122 2.2 5.9 1.0
NE2 A:HIS122 2.2 6.4 1.0
NE2 C:HIS120 2.2 5.1 1.0
NE2 B:HIS120 2.2 5.9 1.0
NE2 B:HIS122 2.3 6.0 1.0
CE1 A:HIS122 3.1 5.7 1.0
CE1 C:HIS122 3.1 4.9 1.0
CD2 A:HIS120 3.2 5.8 1.0
CE1 B:HIS120 3.2 6.0 1.0
CE1 A:HIS120 3.2 6.7 1.0
CD2 A:HIS122 3.2 5.3 1.0
CD2 C:HIS120 3.2 4.9 1.0
CE1 B:HIS122 3.2 5.9 1.0
CE1 C:HIS120 3.2 5.2 1.0
CD2 C:HIS122 3.2 5.1 1.0
CD2 B:HIS120 3.2 5.7 1.0
CD2 B:HIS122 3.3 6.0 1.0
ND1 A:HIS122 4.3 6.0 1.0
ND1 A:HIS120 4.3 6.5 1.0
ND1 C:HIS122 4.3 5.6 1.0
CG A:HIS120 4.3 6.2 1.0
ND1 B:HIS120 4.3 6.2 1.0
CG A:HIS122 4.3 5.8 1.0
CG C:HIS122 4.3 5.4 1.0
ND1 B:HIS122 4.3 6.3 1.0
ND1 C:HIS120 4.4 5.9 1.0
CG C:HIS120 4.4 5.2 1.0
CG B:HIS120 4.4 4.7 1.0
CG B:HIS122 4.4 5.7 1.0

Iron binding site 2 out of 2 in 3aqj

Go back to Iron Binding Sites List in 3aqj
Iron binding site 2 out of 2 in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv


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 A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe135

b:4.8
occ:1.00
NE2 P:HIS122 2.2 5.0 1.0
NE2 Q:HIS120 2.2 5.0 1.0
NE2 R:HIS120 2.2 4.6 1.0
NE2 P:HIS120 2.2 4.9 1.0
NE2 R:HIS122 2.2 4.9 1.0
NE2 Q:HIS122 2.2 5.0 1.0
CE1 P:HIS122 3.1 4.7 1.0
CE1 Q:HIS122 3.1 4.8 1.0
CE1 R:HIS122 3.2 5.2 1.0
CE1 Q:HIS120 3.2 4.7 1.0
CE1 P:HIS120 3.2 5.4 1.0
CD2 Q:HIS120 3.2 5.1 1.0
CE1 R:HIS120 3.2 4.6 1.0
CD2 R:HIS120 3.2 5.2 1.0
CD2 P:HIS120 3.2 5.9 1.0
CD2 Q:HIS122 3.2 4.7 1.0
CD2 P:HIS122 3.2 5.5 1.0
CD2 R:HIS122 3.3 5.9 1.0
ND1 P:HIS122 4.3 5.0 1.0
ND1 Q:HIS120 4.3 5.3 1.0
ND1 Q:HIS122 4.3 5.0 1.0
ND1 R:HIS122 4.3 4.9 1.0
ND1 P:HIS120 4.3 4.8 1.0
ND1 R:HIS120 4.3 5.2 1.0
CG Q:HIS120 4.3 4.9 1.0
CG P:HIS120 4.4 5.3 1.0
CG P:HIS122 4.4 4.8 1.0
CG Q:HIS122 4.4 4.9 1.0
CG R:HIS120 4.4 5.0 1.0
CG R:HIS122 4.4 4.8 1.0

Reference:

E.Yamashita, A.Nakagawa, J.Takahashi, K.Tsunoda, S.Yamada, S.Takeda. The Host-Binding Domain of the P2 Phage Tail Spike Reveals A Trimeric Iron-Binding Structure Acta Crystallogr.,Sect.F V. 67 837 2011.
ISSN: ESSN 1744-3091
PubMed: 21821878
DOI: 10.1107/S1744309111005999
Page generated: Sun Dec 13 15:01:05 2020

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