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Zinc in PDB 7ams: Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2

Protein crystallography data

The structure of Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2, PDB code: 7ams was solved by M.Ferrari, A.Bulek, R.Bughda, R.Jha, M.Welin, A.Svensson, D.T.Logan, A.Sewell, S.Onuoha, M.Pule, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.84, 91.16, 123.32, 90, 94.09, 90
R / Rfree (%) 18 / 22.5

Other elements in 7ams:

The structure of Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2 (pdb code 7ams). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2, PDB code: 7ams:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ams

Go back to Zinc Binding Sites List in 7ams
Zinc binding site 1 out of 3 in the Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:45.0
occ:1.00
OE1 H:GLU62 2.0 48.7 1.0
CD H:GLU62 2.7 46.5 1.0
OE2 H:GLU62 2.8 49.5 1.0
NH1 H:ARG65 3.9 36.4 1.0
CD H:ARG65 4.0 33.1 1.0
CG H:GLU62 4.2 41.8 1.0
O H:HOH528 4.4 36.2 1.0
CB H:ARG65 4.8 33.8 1.0
CZ H:ARG65 4.9 36.2 1.0
NE H:ARG65 4.9 34.7 1.0
CB H:GLU62 4.9 39.7 1.0
CG H:ARG65 5.0 33.1 1.0

Zinc binding site 2 out of 3 in 7ams

Go back to Zinc Binding Sites List in 7ams
Zinc binding site 2 out of 3 in the Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn502

b:41.3
occ:1.00
OD1 L:ASP190 2.1 42.7 1.0
NE2 L:HIS194 2.1 38.7 1.0
CG L:ASP190 3.0 42.2 1.0
CE1 L:HIS194 3.0 39.6 1.0
ZN L:ZN503 3.1 45.4 1.0
CD2 L:HIS194 3.2 38.5 1.0
OD2 L:ASP190 3.2 43.7 1.0
ND1 L:HIS194 4.2 39.7 1.0
CG L:HIS194 4.3 38.6 1.0
O L:ASP190 4.3 41.1 1.0
CB L:ASP190 4.4 40.3 1.0
CA L:ASP190 4.7 40.4 1.0
CD L:LYS193 4.8 47.3 1.0
C L:ASP190 4.8 40.4 1.0
O L:HOH609 4.9 37.0 1.0
CB L:LYS193 4.9 38.1 1.0

Zinc binding site 3 out of 3 in 7ams

Go back to Zinc Binding Sites List in 7ams
Zinc binding site 3 out of 3 in the Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Complex of the Kfn Mutant of Hujovi-1 Fab with Human TRBC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn503

b:45.4
occ:1.00
ZN L:ZN502 3.1 41.3 1.0
OD2 L:ASP190 3.7 43.7 1.0
OE1 L:GLN160 3.7 47.6 1.0
O L:HOH609 3.9 37.0 1.0
NE2 L:HIS194 4.0 38.7 1.0
NE2 L:GLN160 4.2 46.5 1.0
OD1 L:ASP190 4.3 42.7 1.0
CD L:GLN160 4.4 47.0 1.0
CG L:ASP190 4.4 42.2 1.0
CE1 L:HIS194 4.5 39.6 1.0
O L:HOH744 4.6 56.8 1.0
CD2 L:HIS194 4.8 38.5 1.0
CD2 L:LEU186 4.8 43.8 1.0
O L:HOH679 4.9 49.4 1.0

Reference:

M.Ferrari, V.Baldan, P.Wawrzyniecka, A.Bulek, A.Kinna, B.Ma, R.Bugda, Z.Akbar, S.Srivastava, P.Ghongane, I.Gannon, M.Robson, J.Sillibourne, R.Jha, W.Lim, J.Hopkins, M.Welin, S.Surade, M.Dyson, J.Mccafferty, S.Cordoba, S.Thomas, D.Logan, A.Sewell, P.Maciocia, S.Onuoha, M.Pule. Structure-Guided Engineering of Immunotherapies Targeting TRBC1 and TRBC2 in T Cell Malignancies Res Sq 2022.
ISSN: ESSN 2693-5015
DOI: 10.21203/RS.3.RS-1475171/V1
Page generated: Tue Oct 29 16:55:18 2024

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