Magnesium in PDB 6umq: Structure of DUF89

Protein crystallography data

The structure of Structure of DUF89, PDB code: 6umq was solved by J.J.Perry, N.Kenjic, T.N.Dennis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.49 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.140, 194.473, 114.201, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of DUF89 (pdb code 6umq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of DUF89, PDB code: 6umq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6umq

Go back to Magnesium Binding Sites List in 6umq
Magnesium binding site 1 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of DUF89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.9
occ:1.00
O A:HOH722 2.0 11.0 1.0
O A:HOH845 2.1 14.2 1.0
O B:HOH852 2.1 13.6 1.0
O B:HOH728 2.1 13.8 1.0
O A:HOH669 2.1 10.1 1.0
O B:HOH644 2.2 11.6 1.0
O A:LEU99 3.8 10.1 1.0
OE2 B:GLU93 4.0 20.2 1.0
NE2 A:GLN96 4.0 11.4 1.0
O B:HOH605 4.1 19.9 1.0
O A:ASN100 4.2 11.2 1.0
OE1 B:GLU93 4.3 10.9 1.0
OD1 B:ASP86 4.3 16.3 1.0
O A:HOH712 4.3 18.3 1.0
O A:HOH763 4.4 21.5 1.0
O A:GLY104 4.4 10.8 1.0
C A:ASN100 4.4 11.1 1.0
CA A:GLU101 4.6 11.8 1.0
CD B:GLU93 4.6 15.2 1.0
N A:GLU101 4.6 11.8 1.0
C A:LEU99 4.6 11.2 1.0
O B:HOH647 4.7 22.3 1.0
O A:GLN96 5.0 8.7 1.0

Magnesium binding site 2 out of 4 in 6umq

Go back to Magnesium Binding Sites List in 6umq
Magnesium binding site 2 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of DUF89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:9.2
occ:1.00
OD1 A:ASP291 2.0 6.2 1.0
OD1 A:ASP253 2.0 10.4 1.0
OD1 A:ASN254 2.1 10.4 1.0
O A:HOH728 2.1 10.4 1.0
O A:HOH653 2.1 9.4 1.0
O A:HOH811 2.2 10.2 1.0
CG A:ASP291 3.0 5.2 1.0
CG A:ASP253 3.1 12.8 1.0
CG A:ASN254 3.1 10.7 1.0
OD2 A:ASP291 3.4 9.4 1.0
OD2 A:ASP253 3.5 16.5 1.0
ND2 A:ASN254 3.6 20.9 1.0
O A:HOH733 3.7 16.0 1.0
N A:ASN254 4.2 6.4 1.0
CB A:ASN254 4.3 8.3 1.0
CB A:ASP291 4.3 7.7 1.0
O A:PHE288 4.3 8.6 1.0
O A:HOH893 4.3 23.9 1.0
C A:ASP253 4.4 9.1 1.0
CB A:ASP253 4.4 6.4 1.0
CA A:ASN254 4.4 8.9 1.0
N A:ASP291 4.4 6.5 1.0
CA A:ASP291 4.5 6.9 1.0
CA A:ASP253 4.6 6.2 1.0
CB A:SER290 4.7 10.7 1.0
CB A:PHE288 4.7 6.8 1.0
O A:HOH732 4.7 9.3 1.0
C A:SER290 4.8 8.1 1.0
O A:ASP253 4.8 7.1 1.0

Magnesium binding site 3 out of 4 in 6umq

Go back to Magnesium Binding Sites List in 6umq
Magnesium binding site 3 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of DUF89 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:11.7
occ:1.00
O A:HOH710 2.0 11.5 1.0
O B:HOH630 2.1 9.8 1.0
O B:HOH823 2.1 11.4 1.0
O A:HOH874 2.1 13.2 1.0
O A:HOH673 2.2 10.5 1.0
O A:HOH682 2.2 13.2 1.0
O B:LEU99 3.8 11.9 1.0
OE1 A:GLU93 3.9 20.1 1.0
NE2 B:GLN96 4.0 10.3 1.0
O A:HOH626 4.0 24.0 1.0
O B:ASN100 4.2 11.7 1.0
OE2 A:GLU93 4.3 12.0 1.0
O B:HOH640 4.3 16.6 1.0
OD1 A:ASP86 4.3 15.3 1.0
O B:GLY104 4.3 10.5 1.0
C B:ASN100 4.4 11.6 1.0
O B:HOH843 4.5 22.2 1.0
CA B:GLU101 4.5 13.1 1.0
CD A:GLU93 4.6 16.3 1.0
N B:GLU101 4.6 12.2 1.0
C B:LEU99 4.7 12.8 1.0
O A:HOH785 4.9 19.3 1.0
O B:GLN96 4.9 11.1 1.0

Magnesium binding site 4 out of 4 in 6umq

Go back to Magnesium Binding Sites List in 6umq
Magnesium binding site 4 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of DUF89 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:8.7
occ:1.00
OD1 B:ASP291 2.0 8.0 1.0
OD1 B:ASP253 2.1 10.1 1.0
O B:HOH655 2.1 10.5 1.0
OD1 B:ASN254 2.1 11.9 1.0
O B:HOH762 2.1 7.8 1.0
O B:HOH773 2.2 12.4 1.0
CG B:ASP291 3.0 9.5 1.0
CG B:ASP253 3.1 13.4 1.0
CG B:ASN254 3.2 15.8 1.0
OD2 B:ASP291 3.4 11.6 1.0
OD2 B:ASP253 3.5 15.8 1.0
O B:HOH735 3.6 13.9 1.0
ND2 B:ASN254 3.9 23.1 1.0
O B:PHE288 4.3 8.5 1.0
O B:HOH873 4.3 27.8 1.0
N B:ASN254 4.3 7.7 1.0
CB B:ASP291 4.3 8.6 1.0
CB B:ASN254 4.4 11.8 1.0
CB B:ASP253 4.4 8.1 1.0
C B:ASP253 4.4 10.8 1.0
N B:ASP291 4.4 10.3 1.0
CA B:ASN254 4.4 10.1 1.0
CA B:ASP291 4.5 8.3 1.0
CB B:PHE288 4.6 8.2 1.0
CA B:ASP253 4.6 9.4 1.0
O B:HOH714 4.7 10.6 1.0
O B:ASP253 4.8 9.2 1.0
C B:SER290 4.8 11.0 1.0
CB B:SER290 4.9 13.1 1.0

Reference:

T.N.Dennis, N.Kenjic, A.S.Kang, J.D.Lowenson, J.S.Kirkwood, S.G.Clarke, J.J.P.Perry. Human ARMT1 Structure and Substrate Specificity Indicates That It Is A DUF89 Family Damage-Control Phosphatase. J.Struct.Biol. V. 212 07576 2020.
ISSN: ESSN 1095-8657
PubMed: 32682077
DOI: 10.1016/J.JSB.2020.107576
Page generated: Tue Dec 15 01:02:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy