Zinc in PDB 6wuq: Crystal Structure of AJIA1 in Apo Form

Protein crystallography data

The structure of Crystal Structure of AJIA1 in Apo Form, PDB code: 6wuq was solved by F.C.R.Paiva, K.Chan, P.Leadlay, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.82 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.777, 128.777, 101.449, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.4

Other elements in 6wuq:

The structure of Crystal Structure of AJIA1 in Apo Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of AJIA1 in Apo Form (pdb code 6wuq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of AJIA1 in Apo Form, PDB code: 6wuq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6wuq

Go back to Zinc Binding Sites List in 6wuq
Zinc binding site 1 out of 2 in the Crystal Structure of AJIA1 in Apo Form


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 AJIA1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:57.5
occ:1.00
NE2 A:HIS254 2.3 51.5 1.0
SG A:CYS310 2.3 63.4 1.0
SG A:CYS308 2.4 56.6 1.0
SG A:CYS248 2.4 53.6 1.0
CD2 A:HIS254 3.0 52.0 1.0
CB A:CYS248 3.1 51.2 1.0
CB A:CYS308 3.1 52.1 1.0
CB A:CYS310 3.1 52.8 1.0
CE1 A:HIS254 3.4 52.3 1.0
N A:CYS310 4.2 57.9 1.0
CG A:GLU250 4.2 58.5 1.0
CG A:HIS254 4.2 58.5 1.0
CA A:CYS310 4.3 55.1 1.0
ND1 A:HIS254 4.4 51.6 1.0
CB A:ARG252 4.5 53.8 1.0
CB A:GLU250 4.5 52.0 1.0
CA A:CYS308 4.5 59.0 1.0
CA A:CYS248 4.5 53.4 1.0
C A:CYS308 4.7 65.6 1.0
O A:CYS308 4.9 60.5 1.0
O A:ARG252 5.0 52.4 1.0
NE A:ARG252 5.0 79.3 1.0

Zinc binding site 2 out of 2 in 6wuq

Go back to Zinc Binding Sites List in 6wuq
Zinc binding site 2 out of 2 in the Crystal Structure of AJIA1 in Apo Form


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 AJIA1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:69.4
occ:1.00
SG B:CYS248 2.3 62.4 1.0
SG B:CYS310 2.3 66.9 1.0
NE2 B:HIS254 2.4 66.3 1.0
SG B:CYS308 2.5 79.4 1.0
CB B:CYS248 3.0 62.7 1.0
CD2 B:HIS254 3.0 64.2 1.0
CB B:CYS308 3.1 83.8 1.0
CB B:CYS310 3.2 73.9 1.0
CE1 B:HIS254 3.5 72.3 1.0
N B:CYS310 4.2 87.1 1.0
CB B:ARG252 4.3 67.8 1.0
CG B:HIS254 4.3 68.1 1.0
CA B:CYS310 4.3 79.8 1.0
CB B:GLU250 4.4 70.2 1.0
CA B:CYS248 4.5 63.1 1.0
ND1 B:HIS254 4.5 76.0 1.0
CA B:CYS308 4.5 87.0 1.0
O B:ARG252 4.7 66.1 1.0
C B:CYS308 4.8 81.3 1.0
CG B:ARG252 4.8 72.1 1.0
N B:ARG252 4.9 61.7 1.0
N B:CYS248 4.9 57.2 1.0

Reference:

F.C.R.Paiva, K.Chan, M.Samborskyy, A.M.Silber, P.Leadlay, M.V.B.Dias. The Crystal Structure of AJIA1 Reveals A Novel Structural Motion Mechanism in the Adenylate-Forming Enzyme Family Acta Crystallogr.,Sect.D V. 76 1201 2020.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798320013431
Page generated: Wed Dec 16 13:06:38 2020

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