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Magnesium in PDB 5ld1: Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp

Protein crystallography data

The structure of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp, PDB code: 5ld1 was solved by S.Gerhardt, O.Einsle, F.Kemper, N.Schwarzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 118.80 / 2.09
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 168.014, 168.014, 95.032, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp (pdb code 5ld1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp, PDB code: 5ld1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5ld1

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Magnesium binding site 1 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:20.8
occ:1.00
 O2G A:ATP1001 1.9 22.5 1.0
O2B A:ATP1001 2.0 25.2 1.0
OD1 A:ASP66 2.1 20.6 1.0
O1G A:ATP1002 2.2 19.0 1.0
O1A A:ATP1002 2.2 20.4 1.0
O1B A:ATP1002 2.2 20.1 1.0
CG A:ASP66 3.2 24.2 1.0
PB A:ATP1001 3.2 23.9 1.0
PG A:ATP1001 3.2 22.6 1.0
PB A:ATP1002 3.2 21.5 1.0
PG A:ATP1002 3.4 22.0 1.0
O3B A:ATP1001 3.4 22.5 1.0
PA A:ATP1002 3.5 23.8 1.0
O3B A:ATP1002 3.6 23.3 1.0
O3A A:ATP1002 3.6 23.3 1.0
O A:HOH1142 3.8 33.8 1.0
CA A:ASP66 3.9 20.8 1.0
CB A:ASP66 4.0 21.6 1.0
NZ A:LYS70 4.0 17.7 1.0
O1G A:ATP1001 4.0 24.3 1.0
N A:ALA67 4.0 21.0 1.0
OD2 A:ASP66 4.1 32.0 1.0
NH2 A:ARG182 4.1 26.1 1.0
O3A A:ATP1001 4.1 26.0 1.0
O3G A:ATP1002 4.2 18.4 1.0
O1B A:ATP1001 4.2 23.5 1.0
NH2 A:ARG122 4.3 25.4 1.0
O3G A:ATP1001 4.3 25.2 1.0
C5' A:ATP1002 4.4 21.9 1.0
O5' A:ATP1002 4.4 26.6 1.0
O2A A:ATP1002 4.5 27.9 1.0
NH1 A:ARG182 4.5 21.2 1.0
C A:ASP66 4.5 25.0 1.0
O2G A:ATP1002 4.5 22.9 1.0
O2B A:ATP1002 4.6 23.5 1.0
CE A:LYS70 4.7 16.8 1.0
CZ A:ARG182 4.8 33.0 1.0
C3' A:ATP1002 5.0 20.0 1.0
N A:ASP66 5.0 20.5 1.0

Magnesium binding site 2 out of 7 in 5ld1

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Magnesium binding site 2 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:24.4
occ:1.00
 OD1 B:ASP66 2.0 21.5 1.0
O1B B:ATP1001 2.0 25.1 1.0
O1G B:ATP1001 2.0 21.9 1.0
O2G B:ATP1002 2.1 18.4 1.0
O2A B:ATP1002 2.1 19.9 1.0
O2B B:ATP1002 2.3 19.0 1.0
CG B:ASP66 3.2 25.0 1.0
PB B:ATP1002 3.3 18.9 1.0
PB B:ATP1001 3.3 21.2 1.0
PG B:ATP1002 3.4 17.6 1.0
PG B:ATP1001 3.4 22.1 1.0
PA B:ATP1002 3.4 17.9 1.0
O3B B:ATP1001 3.5 19.6 1.0
O3B B:ATP1002 3.6 16.5 1.0
O3A B:ATP1002 3.6 20.7 1.0
CA B:ASP66 3.8 20.0 1.0
O B:HOH1223 3.8 29.6 1.0
CB B:ASP66 4.0 20.9 1.0
N B:ALA67 4.0 20.5 1.0
NH2 B:ARG182 4.0 26.9 1.0
OD2 B:ASP66 4.0 30.5 1.0
NZ B:LYS70 4.1 11.3 1.0
O2G B:ATP1001 4.1 24.5 1.0
O3G B:ATP1002 4.1 18.1 1.0
O3A B:ATP1001 4.3 25.2 1.0
O2B B:ATP1001 4.3 25.0 1.0
C5' B:ATP1002 4.3 22.4 1.0
O5' B:ATP1002 4.3 23.5 1.0
NH1 B:ARG122 4.4 28.1 1.0
NH1 B:ARG182 4.4 18.3 1.0
O1A B:ATP1002 4.4 18.8 1.0
C B:ASP66 4.4 24.6 1.0
O1G B:ATP1002 4.5 19.9 1.0
O3G B:ATP1001 4.5 23.5 1.0
O1B B:ATP1002 4.6 19.1 1.0
CZ B:ARG182 4.7 26.7 1.0
CE B:LYS70 4.7 15.3 1.0
N B:ASP66 5.0 21.1 1.0

Magnesium binding site 3 out of 7 in 5ld1

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Magnesium binding site 3 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:31.7
occ:1.00
 O B:HOH1105 2.5 19.7 1.0
O B:HOH1276 2.6 18.2 1.0
O D:HOH1166 2.7 31.4 1.0
O D:HOH1243 3.0 21.7 1.0
OG1 B:THR95 3.5 15.0 1.0
CB B:THR95 3.7 18.2 1.0
OG1 D:THR95 3.7 18.3 1.0
CB D:THR95 3.8 17.9 1.0
CG2 D:THR95 3.9 10.0 1.0
CG2 B:THR95 3.9 18.6 1.0
CB B:GLN97 4.2 17.4 1.0
CG B:GLN97 4.3 23.7 1.0
CB D:GLN97 4.5 19.3 1.0
CG D:GLN97 4.6 21.8 1.0
O D:HOH1195 4.7 28.2 1.0
O B:HOH1268 4.7 37.4 1.0
O B:HOH1285 4.8 34.3 1.0
N B:GLN97 4.8 16.8 1.0
O D:HOH1236 5.0 34.4 1.0

Magnesium binding site 4 out of 7 in 5ld1

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Magnesium binding site 4 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:37.2
occ:1.00
 OD1 B:ASP127 2.5 22.5 1.0
O B:HOH1195 2.8 23.2 1.0
O B:HOH1258 2.8 26.2 1.0
O B:HOH1312 3.0 23.4 1.0
N6 B:ATP1001 3.5 17.4 1.0
CG B:ASP127 3.6 21.7 1.0
CG B:PRO94 3.7 21.2 1.0
CD2 B:LEU99 3.8 14.9 1.0
O B:HOH1311 3.8 32.9 1.0
O B:HOH1315 3.9 24.0 1.0
O B:HOH1122 4.0 16.9 1.0
O B:HOH1232 4.0 16.7 1.0
OD2 B:ASP127 4.0 24.5 1.0
CB B:TYR103 4.1 16.1 1.0
N1 B:ATP1001 4.2 21.9 1.0
C6 B:ATP1001 4.3 17.3 1.0
CB B:PRO94 4.4 18.8 1.0
CG2 B:VAL131 4.4 22.6 1.0
CB B:ASP127 4.8 15.0 1.0
CA B:TYR103 4.8 14.7 1.0
CD B:PRO94 4.9 17.6 1.0

Magnesium binding site 5 out of 7 in 5ld1

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Magnesium binding site 5 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:25.3
occ:1.00
 O2G C:ATP1002 2.0 28.1 1.0
O2A C:ATP1002 2.0 25.9 1.0
O2B C:ATP1002 2.1 23.3 1.0
O1B C:ATP1001 2.1 27.8 1.0
O1G C:ATP1001 2.2 21.8 1.0
OD1 C:ASP66 2.2 29.8 1.0
PB C:ATP1002 3.0 21.4 1.0
PG C:ATP1002 3.2 23.1 1.0
PA C:ATP1002 3.2 26.2 1.0
O3B C:ATP1002 3.4 22.9 1.0
CG C:ASP66 3.4 31.1 1.0
O3A C:ATP1002 3.4 26.1 1.0
PB C:ATP1001 3.4 26.7 1.0
PG C:ATP1001 3.5 23.6 1.0
O3B C:ATP1001 3.6 23.2 1.0
O C:HOH1166 3.9 35.3 1.0
NH2 C:ARG182 4.0 31.2 1.0
CA C:ASP66 4.0 26.1 1.0
O3G C:ATP1002 4.0 23.9 1.0
N C:ALA67 4.0 26.7 1.0
NZ C:LYS70 4.1 20.6 1.0
CB C:ASP66 4.2 27.6 1.0
O5' C:ATP1002 4.2 29.1 1.0
OD2 C:ASP66 4.2 35.5 1.0
O1A C:ATP1002 4.3 29.2 1.0
C5' C:ATP1002 4.3 27.3 1.0
O3A C:ATP1001 4.3 33.3 1.0
NH2 C:ARG122 4.3 22.6 1.0
O1G C:ATP1002 4.3 21.9 1.0
O2G C:ATP1001 4.4 26.5 1.0
O1B C:ATP1002 4.4 22.1 1.0
O2B C:ATP1001 4.4 26.6 1.0
NH1 C:ARG182 4.4 33.4 1.0
O3G C:ATP1001 4.5 27.3 1.0
C C:ASP66 4.6 31.3 1.0
CE C:LYS70 4.7 26.2 1.0
CZ C:ARG182 4.7 48.9 1.0
C3' C:ATP1002 4.9 23.2 1.0

Magnesium binding site 6 out of 7 in 5ld1

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Magnesium binding site 6 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1005

b:26.6
occ:1.00
 O C:VAL111 2.7 14.7 1.0
O C:GLN109 2.7 16.2 1.0
O C:HOH1266 2.8 35.4 1.0
NE D:ARG101 3.0 20.4 1.0
O C:HOH1121 3.0 37.2 1.0
NE1 D:TRP105 3.6 17.6 1.0
NH2 C:ARG87 3.6 19.5 1.0
C C:GLN110 3.6 18.9 1.0
N C:VAL111 3.6 16.9 1.0
NH1 D:ARG101 3.7 19.1 1.0
C C:GLN109 3.8 16.2 1.0
C C:VAL111 3.8 17.8 1.0
CZ D:ARG101 3.8 27.4 1.0
CD D:ARG101 3.8 21.1 1.0
CA C:GLN110 3.9 15.1 1.0
O C:GLN110 4.1 16.1 1.0
CE2 D:TRP105 4.1 19.5 1.0
N C:GLN110 4.2 14.0 1.0
CZ2 D:TRP105 4.2 18.6 1.0
CA C:VAL111 4.2 15.3 1.0
CG2 C:VAL111 4.4 16.1 1.0
CG D:ARG101 4.4 20.6 1.0
CD1 D:TRP105 4.4 18.3 1.0
O C:HIS108 4.8 19.7 1.0
CZ C:ARG87 4.8 26.9 1.0
NE2 C:GLN109 4.9 13.4 0.5
N C:PRO112 4.9 16.4 1.0
CA C:GLN109 5.0 14.6 0.5
CB C:VAL111 5.0 16.7 1.0

Magnesium binding site 7 out of 7 in 5ld1

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Magnesium binding site 7 out of 7 in the Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:26.8
occ:1.00
 OD1 D:ASP66 2.0 27.2 1.0
O2B D:ATP1001 2.1 29.8 1.0
O2G D:ATP1002 2.1 24.8 1.0
O2G D:ATP1001 2.1 24.0 1.0
O1A D:ATP1002 2.1 23.9 1.0
O1B D:ATP1002 2.2 21.1 1.0
CG D:ASP66 3.2 28.1 1.0
PB D:ATP1002 3.2 22.0 1.0
PB D:ATP1001 3.3 26.6 1.0
PG D:ATP1002 3.3 24.2 1.0
PG D:ATP1001 3.4 24.2 1.0
PA D:ATP1002 3.4 24.5 1.0
O3B D:ATP1001 3.5 25.7 1.0
O3B D:ATP1002 3.6 23.2 1.0
O3A D:ATP1002 3.6 24.4 1.0
O D:HOH1160 3.8 32.5 1.0
CA D:ASP66 3.8 19.5 1.0
N D:ALA67 4.0 22.9 1.0
CB D:ASP66 4.0 19.9 1.0
NH2 D:ARG182 4.0 32.2 1.0
NZ D:LYS70 4.0 18.8 1.0
OD2 D:ASP66 4.1 36.4 1.0
O1G D:ATP1002 4.1 24.9 1.0
O3G D:ATP1001 4.1 29.9 1.0
O3A D:ATP1001 4.3 32.0 1.0
O1B D:ATP1001 4.3 30.1 1.0
O2A D:ATP1002 4.4 26.4 1.0
O5' D:ATP1002 4.4 25.0 1.0
C5' D:ATP1002 4.4 27.1 1.0
NH1 D:ARG182 4.4 26.1 1.0
O1G D:ATP1001 4.4 22.3 1.0
O3G D:ATP1002 4.4 25.4 1.0
NH1 D:ARG122 4.4 25.2 1.0
C D:ASP66 4.5 25.3 1.0
O2B D:ATP1002 4.5 23.6 1.0
CE D:LYS70 4.7 15.3 1.0
CZ D:ARG182 4.7 41.8 1.0
N D:ASP66 5.0 20.5 1.0

Reference:

A.E.Parnell, S.Mordhorst, F.Kemper, M.Giurrandino, J.P.Prince, N.J.Schwarzer, A.Hofer, D.Wohlwend, H.J.Jessen, S.Gerhardt, O.Einsle, P.C.F.Oyston, J.N.Andexer, P.L.Roach. Substrate Recognition and Mechanism Revealed By Ligand-Bound Polyphosphate Kinase 2 Structures. Proc. Natl. Acad. Sci. V. 115 3350 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29531036
DOI: 10.1073/PNAS.1710741115
Page generated: Sun Sep 29 20:04:22 2024

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