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Magnesium in PDB 6d9r: The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)

Enzymatic activity of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)

All present enzymatic activity of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase):
2.4.2.8;

Protein crystallography data

The structure of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase), PDB code: 6d9r was solved by K.A.Satyshur, C.Wolak, B.Anderson, K.Dubiel, J.L.Keck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.19 / 1.64
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.758, 113.758, 56.731, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) (pdb code 6d9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase), PDB code: 6d9r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6d9r

Go back to Magnesium Binding Sites List in 6d9r
Magnesium binding site 1 out of 4 in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:15.0
occ:1.00
 O1A A:PRP202 2.0 13.9 1.0
O1B A:PRP202 2.0 14.1 1.0
O A:HOH367 2.1 18.8 1.0
OD1 A:ASP159 2.1 15.1 1.0
O A:HOH355 2.1 15.7 1.0
O A:HOH406 2.2 19.3 1.0
PA A:PRP202 3.2 16.0 1.0
CG A:ASP159 3.2 16.8 1.0
PB A:PRP202 3.3 15.3 1.0
HH22 A:ARG165 3.3 18.6 1.0
H1 A:PRP202 3.4 21.6 1.0
O3A A:PRP202 3.5 16.4 1.0
HH12 A:ARG165 3.5 17.3 1.0
OD2 A:ASP159 3.5 19.4 1.0
O A:HOH320 3.7 18.1 1.0
H11 A:EDO209 3.8 53.1 1.0
H22 A:EDO209 3.8 40.5 1.0
H A:ASP159 3.8 15.8 1.0
O1 A:PRP202 3.9 18.5 1.0
NH2 A:ARG165 4.0 15.5 1.0
C1 A:PRP202 4.1 18.0 1.0
O A:HOH401 4.1 44.7 1.0
H21 A:EDO209 4.1 40.5 1.0
NH1 A:ARG165 4.2 14.4 1.0
O3B A:PRP202 4.2 15.0 1.0
N3 A:9DG201 4.2 16.7 1.0
HN21 A:9DG201 4.3 22.2 1.0
C2 A:EDO209 4.4 33.8 1.0
O2B A:PRP202 4.4 16.5 1.0
H9 A:9DG201 4.5 26.6 1.0
O2A A:PRP202 4.5 17.4 1.0
CB A:ASP159 4.5 14.2 1.0
CZ A:ARG165 4.5 15.2 1.0
C1 A:EDO209 4.6 44.2 1.0
HH21 A:ARG165 4.6 18.6 1.0
O A:ASP159 4.6 14.9 1.0
N A:ASP159 4.7 13.2 1.0
HO2 A:PRP202 4.7 21.3 1.0
HB3 A:ASP159 4.7 17.0 1.0
O2 A:PRP202 4.8 17.8 1.0
HH11 A:ARG165 4.9 17.3 1.0
O A:HOH356 4.9 31.8 1.0
C2 A:PRP202 4.9 19.1 1.0
N2 A:9DG201 5.0 18.5 1.0

Magnesium binding site 2 out of 4 in 6d9r

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Magnesium binding site 2 out of 4 in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:16.1
occ:1.00
 O A:HOH387 2.0 17.3 1.0
O3B A:PRP202 2.0 15.0 1.0
O A:HOH310 2.1 14.5 1.0
O2 A:PRP202 2.1 17.8 1.0
O3 A:PRP202 2.2 17.3 1.0
O1 A:PRP202 2.3 18.5 1.0
HO3 A:PRP202 2.6 20.8 1.0
HO2 A:PRP202 2.8 21.3 1.0
C2 A:PRP202 2.8 19.1 1.0
C3 A:PRP202 2.9 16.2 1.0
C1 A:PRP202 3.0 18.0 1.0
PB A:PRP202 3.2 15.3 1.0
O3A A:PRP202 3.3 16.4 1.0
H A:GLY44 3.3 19.0 1.0
PA A:PRP202 3.5 16.0 1.0
H3 A:PRP202 3.5 19.4 1.0
H1 A:PRP202 3.7 21.6 1.0
H2 A:PRP202 3.8 22.9 1.0
HG12 A:VAL41 3.8 18.9 1.0
HA3 A:GLY44 4.0 18.0 1.0
C4 A:PRP202 4.0 17.9 1.0
O A:HOH320 4.0 18.1 1.0
OD1 A:ASP100 4.0 19.6 1.0
OE2 A:GLU99 4.0 19.9 1.0
O4 A:PRP202 4.1 16.2 1.0
O1B A:PRP202 4.1 14.1 1.0
O A:HOH361 4.1 36.6 1.0
H4 A:PRP202 4.1 21.5 1.0
O A:LEU42 4.1 18.7 1.0
N A:GLY44 4.2 15.8 1.0
OE1 A:GLU99 4.2 19.6 1.0
O2B A:PRP202 4.2 16.5 1.0
H A:LYS43 4.2 17.4 1.0
O2A A:PRP202 4.3 17.4 1.0
O A:VAL41 4.4 13.1 1.0
HG11 A:VAL41 4.5 18.9 1.0
CD A:GLU99 4.5 20.4 1.0
N A:LYS43 4.5 14.5 1.0
O1A A:PRP202 4.5 13.9 1.0
C A:LEU42 4.5 15.9 1.0
CG1 A:VAL41 4.6 15.7 1.0
CA A:GLY44 4.6 15.0 1.0
HB A:VAL41 4.8 20.1 1.0
CG A:ASP100 4.8 21.8 1.0
OD2 A:ASP100 4.8 22.9 1.0
O A:HOH355 4.8 15.7 1.0
HG21 A:THR107 4.9 25.0 1.0
H A:ALA45 4.9 19.0 1.0

Magnesium binding site 3 out of 4 in 6d9r

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Magnesium binding site 3 out of 4 in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:14.7
occ:1.00
 O2A B:PRP202 2.0 13.9 1.0
O2B B:PRP202 2.0 13.9 1.0
O B:HOH363 2.1 18.2 1.0
OD1 B:ASP159 2.1 15.2 1.0
O B:HOH358 2.1 16.2 1.0
O B:HOH402 2.2 20.1 1.0
CG B:ASP159 3.2 17.9 1.0
PA B:PRP202 3.2 15.7 1.0
PB B:PRP202 3.3 15.2 1.0
HH22 B:ARG165 3.3 17.5 1.0
H1 B:PRP202 3.4 22.8 1.0
O3A B:PRP202 3.5 15.5 1.0
HH12 B:ARG165 3.5 18.1 1.0
OD2 B:ASP159 3.5 18.5 1.0
O B:HOH327 3.7 18.1 1.0
H B:ASP159 3.8 16.0 1.0
O1 B:PRP202 3.9 18.2 1.0
NH2 B:ARG165 4.0 14.6 1.0
C1 B:PRP202 4.1 19.0 1.0
O B:HOH431 4.2 48.1 1.0
NH1 B:ARG165 4.2 15.1 1.0
N3 B:9DG201 4.2 16.4 1.0
O3B B:PRP202 4.2 14.9 1.0
HN21 B:9DG201 4.3 21.1 1.0
O1B B:PRP202 4.4 16.7 1.0
H9 B:9DG201 4.5 27.5 1.0
CB B:ASP159 4.5 13.8 1.0
O1A B:PRP202 4.5 16.8 1.0
CZ B:ARG165 4.5 15.5 1.0
HH21 B:ARG165 4.6 17.5 1.0
O B:ASP159 4.6 15.4 1.0
N B:ASP159 4.6 13.3 1.0
HO2 B:PRP202 4.6 21.9 1.0
O B:HOH421 4.7 34.3 1.0
HB3 B:ASP159 4.7 16.5 1.0
HH11 B:ARG165 4.9 18.1 1.0
O2 B:PRP202 4.9 18.2 1.0
O B:HOH371 4.9 31.0 1.0
C2 B:PRP202 4.9 19.2 1.0
N2 B:9DG201 5.0 17.6 1.0

Magnesium binding site 4 out of 4 in 6d9r

Go back to Magnesium Binding Sites List in 6d9r
Magnesium binding site 4 out of 4 in the The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Substrate-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:16.1
occ:1.00
 O B:HOH384 1.9 17.3 1.0
O3B B:PRP202 2.0 14.9 1.0
O2 B:PRP202 2.1 18.2 1.0
O B:HOH312 2.1 14.4 1.0
O3 B:PRP202 2.2 17.4 1.0
O1 B:PRP202 2.2 18.2 1.0
HO3 B:PRP202 2.4 20.9 1.0
HO2 B:PRP202 2.8 21.9 1.0
C2 B:PRP202 2.8 19.2 1.0
C3 B:PRP202 2.9 16.0 1.0
C1 B:PRP202 3.0 19.0 1.0
PB B:PRP202 3.2 15.2 1.0
O3A B:PRP202 3.3 15.5 1.0
H B:GLY44 3.4 17.9 1.0
PA B:PRP202 3.5 15.7 1.0
H3 B:PRP202 3.5 19.2 1.0
H1 B:PRP202 3.7 22.8 1.0
H2 B:PRP202 3.8 23.1 1.0
HG12 B:VAL41 3.8 20.1 1.0
C4 B:PRP202 4.0 17.2 1.0
O B:HOH327 4.0 18.1 1.0
HA3 B:GLY44 4.0 16.8 1.0
OE2 B:GLU99 4.0 19.8 1.0
OD1 B:ASP100 4.1 19.8 1.0
O4 B:PRP202 4.1 16.1 1.0
O B:HOH342 4.1 39.2 1.0
O2B B:PRP202 4.1 13.9 1.0
O B:LEU42 4.1 18.5 1.0
H4 B:PRP202 4.1 20.7 1.0
N B:GLY44 4.2 14.9 1.0
OE1 B:GLU99 4.2 19.2 1.0
H B:LYS43 4.2 16.5 1.0
O1B B:PRP202 4.2 16.7 1.0
O1A B:PRP202 4.3 16.8 1.0
HG11 B:VAL41 4.4 20.1 1.0
O B:VAL41 4.5 13.1 1.0
CD B:GLU99 4.5 19.7 1.0
O2A B:PRP202 4.5 13.9 1.0
N B:LYS43 4.5 13.7 1.0
C B:LEU42 4.5 14.6 1.0
CG1 B:VAL41 4.5 16.8 1.0
CA B:GLY44 4.6 14.0 1.0
HB B:VAL41 4.8 19.4 1.0
CG B:ASP100 4.8 21.3 1.0
OD2 B:ASP100 4.8 22.7 1.0
O B:HOH358 4.8 16.2 1.0
HG21 B:THR107 4.9 25.6 1.0
H B:ALA45 4.9 18.2 1.0

Reference:

B.W.Anderson, K.Liu, C.Wolak, K.Dubiel, F.She, K.A.Satyshur, J.L.Keck, J.D.Wang. Evolution of (P)Ppgpp-Hprt Regulation Through Diversification of An Allosteric Oligomeric Interaction. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31552824
DOI: 10.7554/ELIFE.47534
Page generated: Mon Sep 30 23:05:59 2024

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