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Iron in PDB 2pms: Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A

Protein crystallography data

The structure of Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A, PDB code: 2pms was solved by D.Chattopadhyay, O.Senkovich, W.J.Cook, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.91
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 130.180, 130.180, 80.800, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.9

Other elements in 2pms:

The structure of Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A (pdb code 2pms). 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 the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A, PDB code: 2pms:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2pms

Go back to Iron Binding Sites List in 2pms
Iron binding site 1 out of 2 in the Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A


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 the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe347

b:18.6
occ:1.00
O1 A:CO3346 1.8 21.1 1.0
OH A:TYR193 1.9 27.4 1.0
OD1 A:ASP61 1.9 25.2 1.0
OH A:TYR93 2.1 20.7 1.0
NE2 A:HIS254 2.2 21.2 1.0
C A:CO3346 2.6 21.4 1.0
O2 A:CO3346 2.7 21.2 1.0
CZ A:TYR193 3.0 27.5 1.0
CG A:ASP61 3.1 23.8 1.0
CZ A:TYR93 3.1 19.9 1.0
CE1 A:HIS254 3.1 21.5 1.0
CD2 A:HIS254 3.3 20.9 1.0
CE2 A:TYR93 3.6 18.9 1.0
CE1 A:TYR193 3.7 27.5 1.0
O3 A:CO3346 3.8 21.7 1.0
CB A:ASP61 3.9 22.1 1.0
CE2 A:TYR193 3.9 27.1 1.0
NH2 A:ARG211 4.0 29.4 1.0
OD2 A:ASP61 4.0 26.2 1.0
CE1 A:TYR93 4.1 19.9 1.0
ND1 A:HIS254 4.3 20.9 1.0
CB A:THR123 4.3 26.2 1.0
CG A:HIS254 4.4 20.8 1.0
CA A:ASP61 4.6 21.6 1.0
OG1 A:THR123 4.6 26.9 1.0
N A:ALA124 4.8 25.5 1.0
N A:THR123 4.8 26.5 1.0
NE A:ARG122 4.9 34.8 1.0
N A:GLY62 4.9 21.8 1.0
CD2 A:TYR93 4.9 19.9 1.0
CZ A:ARG211 4.9 30.2 1.0
NE A:ARG211 5.0 29.1 1.0

Iron binding site 2 out of 2 in 2pms

Go back to Iron Binding Sites List in 2pms
Iron binding site 2 out of 2 in the Crystal Structure of the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A


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 the Complex of Human Lactoferrin N-Lobe and Lactoferrin-Binding Domain of Pneumococcal Surface Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe347

b:18.7
occ:1.00
OH B:TYR193 1.8 27.1 1.0
O1 B:CO3346 1.9 21.3 1.0
OD1 B:ASP61 1.9 25.4 1.0
OH B:TYR93 2.1 20.4 1.0
NE2 B:HIS254 2.2 20.1 1.0
O2 B:CO3346 2.6 21.4 1.0
C B:CO3346 2.6 21.6 1.0
CZ B:TYR193 3.0 27.3 1.0
CE1 B:HIS254 3.0 20.7 1.0
CZ B:TYR93 3.1 20.1 1.0
CG B:ASP61 3.1 24.1 1.0
CD2 B:HIS254 3.2 20.8 1.0
CE2 B:TYR93 3.7 19.6 1.0
CE1 B:TYR193 3.7 27.6 1.0
O3 B:CO3346 3.8 22.2 1.0
CE2 B:TYR193 3.9 27.0 1.0
CB B:ASP61 4.0 22.1 1.0
OD2 B:ASP61 4.0 26.9 1.0
NH2 B:ARG211 4.1 28.8 1.0
CE1 B:TYR93 4.2 19.8 1.0
ND1 B:HIS254 4.2 20.6 1.0
CB B:THR123 4.3 26.5 1.0
CG B:HIS254 4.3 20.7 1.0
OG1 B:THR123 4.6 27.3 1.0
CA B:ASP61 4.7 21.8 1.0
N B:ALA124 4.7 25.8 1.0
N B:THR123 4.8 27.0 1.0
NE B:ARG122 4.9 35.6 1.0
NE B:ARG211 4.9 29.7 1.0
CZ B:ARG211 5.0 30.3 1.0
CD2 B:TYR93 5.0 19.7 1.0

Reference:

O.Senkovich, W.J.Cook, S.Mirza, S.K.Hollingshead, I.I.Protasevich, D.E.Briles, D.Chattopadhyay. Structure of A Complex of Human Lactoferrin N-Lobe with Pneumococcal Surface Protein A Provides Insight Into Microbial Defense Mechanism. J.Mol.Biol. V. 370 701 2007.
ISSN: ISSN 0022-2836
PubMed: 17543335
DOI: 10.1016/J.JMB.2007.04.075
Page generated: Sun Dec 13 14:51:15 2020

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