Atomistry » Iron » PDB 3crv-3dby » 3d1k
Atomistry »
  Iron »
    PDB 3crv-3dby »
      3d1k »

Iron in PDB 3d1k: R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State

Protein crystallography data

The structure of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State, PDB code: 3d1k was solved by L.Vitagliano, A.Vergara, G.Bonomi, A.Merlino, L.Mazzarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.458, 87.664, 55.502, 90.00, 99.16, 90.00
R / Rfree (%) 16.7 / 20.2

Iron Binding Sites:

The binding sites of Iron atom in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State (pdb code 3d1k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State, PDB code: 3d1k:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3d1k

Go back to Iron Binding Sites List in 3d1k
Iron binding site 1 out of 2 in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:15.7
occ:1.00
FE A:HEM200 0.0 15.7 1.0
C A:CMO199 1.9 16.4 1.0
ND A:HEM200 2.0 16.5 1.0
NC A:HEM200 2.0 15.3 1.0
NA A:HEM200 2.0 15.5 1.0
NB A:HEM200 2.0 15.8 1.0
NE2 A:HIS88 2.0 14.8 1.0
O A:CMO199 3.0 25.0 1.0
CE1 A:HIS88 3.0 16.1 1.0
C1D A:HEM200 3.0 16.6 1.0
C1C A:HEM200 3.0 15.0 1.0
C4C A:HEM200 3.0 15.8 1.0
C4D A:HEM200 3.1 16.5 1.0
C4B A:HEM200 3.1 15.8 1.0
C4A A:HEM200 3.1 16.7 1.0
C1A A:HEM200 3.1 16.3 1.0
C1B A:HEM200 3.1 16.1 1.0
CD2 A:HIS88 3.1 14.5 1.0
CHD A:HEM200 3.4 17.1 1.0
CHC A:HEM200 3.4 14.7 1.0
CHA A:HEM200 3.4 16.9 1.0
CHB A:HEM200 3.5 16.2 1.0
ND1 A:HIS88 4.2 16.4 1.0
C3D A:HEM200 4.2 18.4 1.0
C3C A:HEM200 4.3 15.4 1.0
C2C A:HEM200 4.3 15.1 1.0
C2D A:HEM200 4.3 18.0 1.0
C3A A:HEM200 4.3 17.5 1.0
C2A A:HEM200 4.3 17.9 1.0
C2B A:HEM200 4.3 16.8 1.0
C3B A:HEM200 4.3 15.9 1.0
CG A:HIS88 4.3 14.7 1.0
NE2 A:HIS59 4.3 19.9 1.0
CG2 A:VAL63 4.8 24.8 1.0

Iron binding site 2 out of 2 in 3d1k

Go back to Iron Binding Sites List in 3d1k
Iron binding site 2 out of 2 in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:24.5
occ:1.00
FE B:HEM400 0.0 24.5 1.0
NA B:HEM400 2.0 23.6 1.0
NC B:HEM400 2.0 24.6 1.0
ND B:HEM400 2.0 24.4 1.0
NB B:HEM400 2.0 25.0 1.0
NE2 B:HIS92 2.1 22.2 1.0
O B:HOH399 2.7 26.5 0.6
C4C B:HEM400 3.0 22.8 1.0
C1C B:HEM400 3.0 24.6 1.0
C1A B:HEM400 3.0 25.4 1.0
C4A B:HEM400 3.0 26.3 1.0
C1D B:HEM400 3.0 24.9 1.0
CE1 B:HIS92 3.1 22.3 1.0
C4B B:HEM400 3.1 26.5 1.0
C4D B:HEM400 3.1 24.3 1.0
C1B B:HEM400 3.1 26.4 1.0
CD2 B:HIS92 3.2 22.5 1.0
CHC B:HEM400 3.4 25.1 1.0
CHD B:HEM400 3.4 25.3 1.0
CHA B:HEM400 3.4 25.1 1.0
CHB B:HEM400 3.5 26.2 1.0
ND1 B:HIS92 4.2 22.4 1.0
C3C B:HEM400 4.2 23.7 1.0
C2A B:HEM400 4.2 28.4 1.0
C2C B:HEM400 4.3 24.1 1.0
C3A B:HEM400 4.3 26.9 1.0
C3D B:HEM400 4.3 25.4 1.0
CG2 B:VAL67 4.3 30.9 1.0
C2D B:HEM400 4.3 27.0 1.0
C3B B:HEM400 4.3 26.4 1.0
CG B:HIS92 4.3 20.9 1.0
C2B B:HEM400 4.3 25.8 1.0
NE2 B:HIS63 4.4 28.2 1.0

Reference:

L.Vitagliano, A.Vergara, G.Bonomi, A.Merlino, C.Verde, G.Di Prisco, B.D.Howes, G.Smulevich, L.Mazzarella. Spectroscopic and Crystallographic Characterization of A Tetrameric Hemoglobin Oxidation Reveals Structural Features of the Functional Intermediate Relaxed/Tense State. J.Am.Chem.Soc. V. 130 10527 2008.
ISSN: ISSN 0002-7863
PubMed: 18642904
DOI: 10.1021/JA803363P
Page generated: Sun Aug 4 08:44:38 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy