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Magnesium in PDB 4w5j: New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A

Enzymatic activity of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A

All present enzymatic activity of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A:
2.7.4.3;

Protein crystallography data

The structure of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A, PDB code: 4w5j was solved by T.T.Thach, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.908, 62.298, 63.022, 101.89, 112.59, 89.86
R / Rfree (%) 25.7 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A (pdb code 4w5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A, PDB code: 4w5j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4w5j

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Magnesium binding site 1 out of 4 in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:21.1
occ:1.00
 O1G A:AP5302 2.2 15.2 1.0
O2D A:AP5302 2.2 16.6 1.0
O A:HOH512 2.3 24.0 1.0
O A:HOH527 2.5 32.8 1.0
O A:HOH508 2.5 25.6 1.0
O A:HOH506 2.8 19.0 1.0
PG A:AP5302 3.3 16.6 1.0
PD A:AP5302 3.4 15.5 1.0
HA3 A:GLY14 3.4 16.1 1.0
H A:GLY14 3.5 16.3 1.0
HH12 A:ARG156 3.5 17.4 1.0
O3B A:AP5302 3.7 23.0 1.0
O3G A:AP5302 3.7 13.5 1.0
HH12 A:ARG128 3.8 19.7 1.0
N A:GLY14 4.0 13.6 1.0
CA A:GLY14 4.1 13.4 1.0
HH22 A:ARG36 4.1 22.9 1.0
HB2 A:LYS13 4.1 21.7 1.0
HA2 A:GLY14 4.2 16.1 1.0
NH1 A:ARG156 4.2 14.5 1.0
O1A A:AP5302 4.3 19.3 1.0
HH11 A:ARG156 4.4 17.4 1.0
O3D A:AP5302 4.4 16.8 1.0
O A:HOH529 4.4 25.4 1.0
HE3 A:LYS13 4.5 33.2 1.0
NH1 A:ARG128 4.5 16.4 1.0
O A:HOH553 4.5 42.3 1.0
O1D A:AP5302 4.5 17.4 1.0
OD2 A:ASP85 4.6 21.6 1.0
O2E A:AP5302 4.6 15.5 1.0
O3A A:AP5302 4.6 24.5 1.0
HH11 A:ARG128 4.6 19.7 1.0
O2A A:AP5302 4.6 22.1 1.0
O2G A:AP5302 4.6 18.2 1.0
PB A:AP5302 4.7 24.7 1.0
O A:HOH566 4.7 29.5 1.0
PA A:AP5302 4.8 19.9 1.0
NH2 A:ARG36 4.8 19.1 1.0
OD1 A:ASP85 4.9 23.2 1.0
PE A:AP5302 4.9 12.5 1.0
O A:HOH505 4.9 24.0 1.0
O A:HOH574 4.9 40.6 1.0
O1E A:AP5302 5.0 13.6 1.0

Magnesium binding site 2 out of 4 in 4w5j

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Magnesium binding site 2 out of 4 in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:20.8
occ:1.00
 O2G B:AP5302 2.2 16.7 1.0
O2B B:AP5302 2.3 14.6 1.0
O B:HOH492 2.5 26.4 1.0
O B:HOH497 2.5 27.0 1.0
O B:HOH482 2.6 22.3 1.0
O B:HOH480 2.6 16.1 1.0
PG B:AP5302 3.4 16.8 1.0
H B:GLY14 3.4 14.0 1.0
HA3 B:GLY14 3.4 13.8 1.0
PB B:AP5302 3.5 15.5 1.0
HH12 B:ARG156 3.5 16.8 1.0
O3G B:AP5302 3.6 26.1 1.0
O3B B:AP5302 3.8 14.2 1.0
HH12 B:ARG128 3.8 17.2 1.0
N B:GLY14 3.9 11.7 1.0
CA B:GLY14 4.0 11.5 1.0
HH22 B:ARG36 4.1 21.1 1.0
HB2 B:LYS13 4.1 20.9 1.0
HA2 B:GLY14 4.2 13.8 1.0
NH1 B:ARG156 4.2 14.0 1.0
O B:HOH496 4.3 22.4 1.0
O B:HOH545 4.3 38.9 1.0
O1E B:AP5302 4.3 18.8 1.0
HH11 B:ARG156 4.4 16.8 1.0
O3A B:AP5302 4.4 16.7 1.0
HE3 B:LYS13 4.4 34.4 1.0
NH1 B:ARG128 4.5 14.4 1.0
O B:HOH567 4.5 58.1 1.0
O2A B:AP5302 4.5 13.4 1.0
O B:HOH503 4.6 27.5 1.0
OD2 B:ASP85 4.6 24.2 1.0
O1B B:AP5302 4.6 17.7 1.0
HH11 B:ARG128 4.6 17.2 1.0
O1G B:AP5302 4.7 18.7 1.0
O2E B:AP5302 4.7 22.6 1.0
NH2 B:ARG36 4.8 17.6 1.0
O3D B:AP5302 4.8 30.1 1.0
OD1 B:ASP85 4.8 25.1 1.0
PD B:AP5302 4.8 27.8 1.0
PA B:AP5302 4.8 10.8 1.0
PE B:AP5302 4.9 20.2 1.0

Magnesium binding site 3 out of 4 in 4w5j

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Magnesium binding site 3 out of 4 in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:24.1
occ:1.00
 O1G C:AP5302 2.2 19.4 1.0
O2D C:AP5302 2.3 15.0 1.0
O C:HOH528 2.4 30.4 1.0
O C:HOH510 2.4 23.8 1.0
O C:HOH516 2.4 28.5 1.0
O C:HOH502 2.8 20.4 1.0
PG C:AP5302 3.4 19.5 1.0
HH12 C:ARG156 3.5 18.0 1.0
HA3 C:GLY14 3.5 14.8 1.0
PD C:AP5302 3.5 15.9 1.0
H C:GLY14 3.6 15.6 1.0
O3B C:AP5302 3.7 26.1 1.0
O3G C:AP5302 3.8 15.7 1.0
HH12 C:ARG128 3.9 18.5 1.0
HH22 C:ARG36 4.0 25.2 1.0
N C:GLY14 4.1 13.0 1.0
O C:HOH544 4.1 28.0 1.0
CA C:GLY14 4.1 12.3 1.0
O1A C:AP5302 4.2 17.3 1.0
HB2 C:LYS13 4.2 22.7 1.0
O C:HOH535 4.2 35.4 1.0
NH1 C:ARG156 4.2 15.0 1.0
HA2 C:GLY14 4.3 14.8 1.0
HH11 C:ARG156 4.4 18.0 1.0
HE2 C:LYS13 4.4 43.9 1.0
O2E C:AP5302 4.5 15.7 1.0
O3D C:AP5302 4.5 18.7 1.0
NH1 C:ARG128 4.5 15.4 1.0
O C:HOH589 4.6 45.8 1.0
OD2 C:ASP85 4.6 25.5 1.0
O2A C:AP5302 4.6 23.7 1.0
O1D C:AP5302 4.6 18.5 1.0
O C:HOH547 4.6 29.5 1.0
HH11 C:ARG128 4.6 18.5 1.0
O3A C:AP5302 4.7 25.3 1.0
O2G C:AP5302 4.7 18.8 1.0
NH2 C:ARG36 4.7 21.0 1.0
PA C:AP5302 4.7 20.5 1.0
PB C:AP5302 4.9 29.4 1.0
HH21 C:ARG36 4.9 25.2 1.0
OD1 C:ASP85 4.9 24.9 1.0
PE C:AP5302 4.9 13.4 1.0

Magnesium binding site 4 out of 4 in 4w5j

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Magnesium binding site 4 out of 4 in the New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of New Structural Conformations of Adenylate Kinase From Streptococcus Pneumoniae D39 with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:25.3
occ:1.00
 O1G D:AP5302 2.2 21.4 1.0
O D:HOH514 2.2 31.1 1.0
O2D D:AP5302 2.3 17.3 1.0
O D:HOH506 2.4 27.5 1.0
O D:HOH575 2.4 42.7 1.0
O D:HOH495 3.1 23.9 1.0
PG D:AP5302 3.3 21.0 1.0
PD D:AP5302 3.5 18.0 1.0
HA3 D:GLY14 3.5 16.1 1.0
HH12 D:ARG156 3.5 22.2 1.0
H D:GLY14 3.6 17.3 1.0
O3B D:AP5302 3.7 27.1 1.0
O3G D:AP5302 3.7 17.0 1.0
HH12 D:ARG128 3.9 23.8 1.0
HH22 D:ARG36 4.0 25.7 1.0
N D:GLY14 4.1 14.4 1.0
HB2 D:LYS13 4.1 26.2 1.0
CA D:GLY14 4.1 13.4 1.0
O1A D:AP5302 4.2 23.6 1.0
O D:HOH579 4.3 39.1 1.0
HA2 D:GLY14 4.3 16.1 1.0
NH1 D:ARG156 4.3 18.5 1.0
HH11 D:ARG156 4.5 22.2 1.0
O1D D:AP5302 4.5 19.2 1.0
O2A D:AP5302 4.5 27.4 1.0
O D:HOH551 4.5 34.6 1.0
O3D D:AP5302 4.5 19.0 1.0
O3A D:AP5302 4.5 28.6 1.0
HE2 D:LYS13 4.5 54.8 1.0
O2E D:AP5302 4.6 17.9 1.0
NH1 D:ARG128 4.6 19.8 1.0
O2G D:AP5302 4.6 19.7 1.0
PA D:AP5302 4.6 26.3 1.0
NH2 D:ARG36 4.7 21.4 1.0
PB D:AP5302 4.7 32.7 1.0
HH11 D:ARG128 4.7 23.8 1.0
O D:HOH550 4.8 29.6 1.0
OD2 D:ASP85 4.8 25.7 1.0
HH21 D:ARG36 4.8 25.7 1.0
OD1 D:ASP85 4.9 25.0 1.0
PE D:AP5302 4.9 15.1 1.0
O D:HOH490 4.9 27.9 1.0
O D:HOH535 5.0 38.8 1.0
HG D:SER30 5.0 26.0 1.0

Reference:

T.T.Thach, S.Lee. New Crystal Structures of Adenylate Kinase From Streptococcus Pneumoniae D39 in Two Conformations. Acta Crystallogr.,Sect.F V. 70 1468 2014.
ISSN: ESSN 2053-230X
PubMed: 25372811
DOI: 10.1107/S2053230X14020718
Page generated: Tue Aug 12 00:53:47 2025

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