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Zinc in PDB 6ggm: Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe.

Protein crystallography data

The structure of Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe., PDB code: 6ggm was solved by L.C.Walters, G.M.Gillespie, A.J.Mcmichael, D.Rozbesky, E.Y.Jones, K.Harlos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.18 / 2.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.930, 66.041, 72.104, 102.30, 101.22, 109.70
R / Rfree (%) 18 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe. (pdb code 6ggm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe., PDB code: 6ggm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ggm

Go back to Zinc Binding Sites List in 6ggm
Zinc binding site 1 out of 4 in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:16.3
occ:1.00
OE1 C:GLU183 2.0 12.3 1.0
OE2 A:GLU183 2.0 9.9 1.0
NE2 C:HIS181 2.1 13.3 1.0
NE2 A:HIS181 2.2 10.6 1.0
CD2 C:HIS181 2.9 13.0 1.0
CD A:GLU183 3.0 12.5 1.0
CD2 A:HIS181 3.1 12.9 1.0
CD C:GLU183 3.1 15.3 1.0
CE1 C:HIS181 3.1 14.4 1.0
CE1 A:HIS181 3.3 12.6 1.0
OE1 A:GLU183 3.5 16.6 1.0
OE2 C:GLU183 3.6 14.8 1.0
CG C:HIS181 4.1 16.2 1.0
ND1 C:HIS181 4.2 16.1 1.0
CG A:HIS181 4.3 12.9 1.0
O A:LEU182 4.3 14.6 1.0
ND1 A:HIS181 4.3 15.0 1.0
CG A:GLU183 4.4 10.0 1.0
CG C:GLU183 4.4 17.4 1.0
O C:LEU182 4.5 9.6 1.0
CB C:GLU183 4.6 9.4 1.0
CA A:GLU183 4.6 10.5 1.0
CB A:GLU183 4.6 6.7 1.0
CA C:GLU183 4.7 11.4 1.0
CD A:PRO184 4.9 8.8 1.0

Zinc binding site 2 out of 4 in 6ggm

Go back to Zinc Binding Sites List in 6ggm
Zinc binding site 2 out of 4 in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.7
occ:1.00
NZ P:LYS5 2.0 13.8 1.0
ND1 A:HIS155 2.1 12.7 1.0
OE2 A:GLU152 2.3 16.6 1.0
CE P:LYS5 2.7 11.5 1.0
CD A:GLU152 2.8 17.7 1.0
OE1 A:GLU152 2.9 19.5 1.0
CE1 A:HIS155 3.0 16.7 1.0
CG A:HIS155 3.1 14.2 1.0
CB A:HIS155 3.5 10.4 1.0
CD P:LYS5 4.0 17.1 1.0
NE2 A:HIS155 4.1 21.5 1.0
CD2 A:HIS155 4.2 17.0 1.0
CG A:GLU152 4.2 15.1 1.0
CA A:GLU152 4.3 11.9 1.0
CB A:GLU152 4.5 12.8 1.0
O A:ALA150 4.7 18.9 1.0
O A:GLU152 4.9 16.1 1.0

Zinc binding site 3 out of 4 in 6ggm

Go back to Zinc Binding Sites List in 6ggm
Zinc binding site 3 out of 4 in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:94.5
occ:1.00
OD2 A:ASP196 2.5 60.0 1.0
CD2 A:HIS197 2.7 61.8 1.0
OD1 A:ASP196 2.8 68.9 1.0
CG A:ASP196 2.9 61.1 1.0
CG A:HIS197 3.2 51.9 1.0
CB A:HIS197 3.3 51.7 1.0
NE2 A:HIS197 3.7 72.3 1.0
N A:HIS197 4.0 51.7 1.0
CA A:HIS197 4.3 56.2 1.0
ND1 A:HIS197 4.3 62.1 1.0
CB A:ASP196 4.4 47.1 1.0
CE1 A:HIS197 4.6 61.9 1.0
C A:ASP196 4.7 54.5 1.0
CA A:ASP196 4.9 54.7 1.0
N A:ASP196 5.0 53.2 1.0

Zinc binding site 4 out of 4 in 6ggm

Go back to Zinc Binding Sites List in 6ggm
Zinc binding site 4 out of 4 in the Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hla-E*01:03 in Complex with the MTB44 Peptide Variant: MTB44*P2-Phe. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.9
occ:1.00
OD2 C:ASP196 2.2 83.8 1.0
OD1 C:ASP196 2.3 60.7 1.0
CG C:ASP196 2.5 68.9 1.0
CD2 C:HIS197 3.6 55.1 1.0
CB C:HIS197 4.0 46.7 1.0
CB C:ASP196 4.0 60.9 1.0
CG C:HIS197 4.0 48.6 1.0
N C:HIS197 4.2 53.3 1.0
NE2 C:HIS197 4.7 47.9 1.0
C C:ASP196 4.7 51.6 1.0
CA C:ASP196 4.7 59.5 1.0
CA C:HIS197 4.7 52.6 1.0
N C:ASP196 4.9 56.0 1.0

Reference:

L.C.Walters, K.Harlos, S.Brackenridge, D.Rozbesky, J.R.Barrett, V.Jain, T.S.Walter, C.A.O'callaghan, P.Borrow, M.Toebes, S.G.Hansen, J.Sacha, S.Abdulhaqq, J.M.Greene, K.Fruh, E.Marshall, L.J.Picker, E.Y.Jones, A.J.Mcmichael, G.M.Gillespie. Pathogen-Derived Hla-E Bound Epitopes Reveal Broad Primary Anchor Pocket Tolerability and Conformationally Malleable Peptide Binding. Nat Commun V. 9 3137 2018.
ISSN: ESSN 2041-1723
PubMed: 30087334
DOI: 10.1038/S41467-018-05459-Z
Page generated: Mon Oct 28 21:50:47 2024

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