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Magnesium in PDB 2zdh: Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8

Enzymatic activity of Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8

All present enzymatic activity of Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8, PDB code: 2zdh was solved by Y.Kitamuta, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.946, 105.394, 199.748, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 (pdb code 2zdh). 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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8, PDB code: 2zdh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2zdh

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Magnesium binding site 1 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg811

b:26.5
occ:1.00
 O A:HOH835 2.3 22.1 1.0
OD1 A:ASN284 2.3 18.0 1.0
OE1 A:GLU282 2.3 17.1 1.0
O A:HOH813 2.3 29.2 1.0
O3B A:ADP701 2.6 11.9 1.0
OE2 A:GLU282 2.6 14.1 1.0
CD A:GLU282 2.8 17.8 1.0
O A:HOH859 3.0 15.3 1.0
CG A:ASN284 3.5 15.7 1.0
PB A:ADP701 3.8 15.4 1.0
O A:HOH884 3.9 25.1 1.0
O A:HOH1000 4.0 17.2 1.0
O2B A:ADP701 4.0 16.1 1.0
ND2 A:ASN284 4.0 17.8 1.0
NZ A:LYS116 4.1 16.8 1.0
O A:THR157 4.1 16.9 1.0
CG A:GLU282 4.3 15.1 1.0
MG A:MG812 4.3 21.9 1.0
N A:DAL801 4.4 17.5 1.0
O A:HOH856 4.4 21.2 1.0
OXT A:DAL801 4.4 28.8 1.0
CA A:GLY158 4.5 16.3 1.0
O1B A:ADP701 4.5 14.3 1.0
CB A:ASN284 4.7 15.8 1.0
O A:HOH834 4.7 18.4 1.0
O A:HOH922 4.7 26.6 1.0
O A:LEU283 4.9 13.7 1.0
O A:HOH889 5.0 29.9 1.0

Magnesium binding site 2 out of 7 in 2zdh

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Magnesium binding site 2 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg812

b:21.9
occ:1.00
 O A:HOH999 2.2 16.4 1.0
O2A A:ADP701 2.2 15.4 1.0
O2B A:ADP701 2.2 16.1 1.0
OE2 A:GLU282 2.2 14.1 1.0
O A:HOH1000 2.3 17.2 1.0
O A:HOH998 2.4 13.5 1.0
CD A:GLU282 3.4 17.8 1.0
PB A:ADP701 3.4 15.4 1.0
O A:HOH873 3.5 22.6 1.0
PA A:ADP701 3.6 14.4 1.0
O A:HOH835 3.6 22.1 1.0
OD2 A:ASP270 3.6 16.4 1.0
O3B A:ADP701 3.8 11.9 1.0
NZ A:LYS228 3.9 11.2 1.0
ND2 A:ASN281 3.9 15.2 1.0
CG A:GLU282 4.0 15.1 1.0
O3A A:ADP701 4.0 14.9 1.0
O A:HOH845 4.2 18.3 1.0
O A:HOH834 4.3 18.4 1.0
MG A:MG811 4.3 26.5 1.0
C5' A:ADP701 4.3 12.5 1.0
OE1 A:GLU282 4.4 17.1 1.0
NH1 A:ARG268 4.4 11.9 1.0
O3' A:ADP701 4.5 15.1 1.0
O1A A:ADP701 4.5 15.1 1.0
O5' A:ADP701 4.5 14.2 1.0
CG A:ASP270 4.6 16.4 1.0
ND2 A:ASN284 4.6 17.8 1.0
O1B A:ADP701 4.7 14.3 1.0
CE A:LYS228 4.8 12.8 1.0
C3' A:ADP701 4.9 13.8 1.0
CB A:ASP270 5.0 13.2 1.0
OD1 A:ASN284 5.0 18.0 1.0

Magnesium binding site 3 out of 7 in 2zdh

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Magnesium binding site 3 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg813

b:18.9
occ:1.00
 O2B B:ADP702 2.1 18.3 1.0
O2A B:ADP702 2.1 16.5 1.0
O B:HOH981 2.2 14.5 1.0
OE2 B:GLU282 2.2 14.6 1.0
O B:HOH988 2.3 18.2 1.0
O B:HOH987 2.3 15.2 1.0
CD B:GLU282 3.3 17.2 1.0
PB B:ADP702 3.5 18.4 1.0
PA B:ADP702 3.5 16.3 1.0
O B:HOH983 3.8 13.2 1.0
O3A B:ADP702 3.9 17.5 1.0
OE1 B:GLU282 4.0 15.3 1.0
OD2 B:ASP270 4.0 13.2 1.0
ND2 B:ASN281 4.0 14.9 1.0
OD1 B:ASN284 4.2 13.0 1.0
O3B B:ADP702 4.3 20.6 1.0
CB B:GLU282 4.4 13.2 1.0
CG B:GLU282 4.4 12.4 1.0
O5' B:ADP702 4.4 19.4 1.0
C5' B:ADP702 4.5 16.0 1.0
O1A B:ADP702 4.5 16.5 1.0
O1B B:ADP702 4.5 18.6 1.0
NZ B:LYS116 4.7 19.2 1.0
ND2 B:ASN284 4.9 15.0 1.0
NH2 B:ARG268 5.0 13.3 1.0

Magnesium binding site 4 out of 7 in 2zdh

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Magnesium binding site 4 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg814

b:21.1
occ:1.00
 OE1 B:GLU282 2.1 15.3 1.0
O B:HOH986 2.2 16.0 1.0
O B:HOH983 2.3 13.2 1.0
O B:HOH982 2.3 16.9 1.0
O B:HOH984 2.3 22.6 1.0
O B:HOH985 2.3 13.4 1.0
CD B:GLU282 3.3 17.2 1.0
O B:HOH887 3.7 31.1 1.0
OE2 B:GLU282 3.9 14.6 1.0
OD1 B:ASN284 3.9 13.0 1.0
O B:HOH831 4.0 12.1 1.0
O3B B:ADP702 4.1 20.6 1.0
O B:HOH835 4.1 16.8 1.0
OE2 B:GLU87 4.2 16.1 1.0
O2B B:ADP702 4.4 18.3 1.0
CG B:GLU282 4.5 12.4 1.0
O B:HOH848 4.5 16.5 1.0
O B:HOH981 4.6 14.5 1.0
OE1 B:GLU87 4.6 14.5 1.0
CD B:GLU87 4.7 16.3 1.0
SD B:MET114 4.7 19.0 1.0
CE B:MET114 4.8 19.0 1.0
PB B:ADP702 4.9 18.4 1.0
O B:HOH851 4.9 27.0 1.0
NZ B:LYS116 4.9 19.2 1.0
CG B:ASN284 4.9 13.8 1.0
CA B:GLY158 5.0 27.4 1.0

Magnesium binding site 5 out of 7 in 2zdh

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Magnesium binding site 5 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg815

b:24.6
occ:1.00
 O2B C:ADP703 2.2 22.3 1.0
O C:HOH955 2.2 18.5 1.0
OE2 C:GLU282 2.2 19.7 1.0
O2A C:ADP703 2.2 22.1 1.0
O C:HOH954 2.3 18.7 1.0
O C:HOH956 2.3 17.9 1.0
CD C:GLU282 3.2 22.6 1.0
PB C:ADP703 3.5 21.9 1.0
O C:HOH960 3.6 18.0 1.0
PA C:ADP703 3.7 21.0 1.0
OD2 C:ASP270 3.8 15.2 1.0
OE1 C:GLU282 3.8 21.5 1.0
O3A C:ADP703 4.1 21.3 1.0
ND2 C:ASN281 4.1 17.5 1.0
O3B C:ADP703 4.2 25.3 1.0
OD1 C:ASN284 4.2 14.9 1.0
CG C:GLU282 4.3 20.8 1.0
CB C:GLU282 4.3 19.8 1.0
O C:HOH908 4.3 34.6 1.0
C5' C:ADP703 4.5 20.2 1.0
O5' C:ADP703 4.6 21.3 1.0
O1A C:ADP703 4.6 18.6 1.0
O1B C:ADP703 4.6 22.8 1.0
O C:HOH948 4.7 43.5 1.0
ND2 C:ASN284 4.9 16.5 1.0
NH2 C:ARG268 4.9 17.8 1.0
CG C:ASP270 4.9 17.5 1.0
CG C:ASN284 5.0 16.1 1.0

Magnesium binding site 6 out of 7 in 2zdh

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Magnesium binding site 6 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg816

b:25.2
occ:1.00
 OE1 C:GLU282 2.2 21.5 1.0
O C:HOH959 2.3 17.6 1.0
O C:HOH960 2.3 18.0 1.0
O C:HOH961 2.3 24.2 1.0
O C:HOH957 2.3 20.0 1.0
O C:HOH958 2.4 18.1 1.0
CD C:GLU282 3.4 22.6 1.0
O C:HOH863 3.8 34.8 1.0
OD1 C:ASN284 3.9 14.9 1.0
OE2 C:GLU282 4.0 19.7 1.0
OE1 C:GLU87 4.0 19.2 1.0
O C:HOH821 4.1 15.6 1.0
O3B C:ADP703 4.1 25.3 1.0
O C:HOH820 4.1 16.1 1.0
O C:THR157 4.3 36.1 1.0
CG C:GLU282 4.5 20.8 1.0
O C:HOH827 4.5 19.3 1.0
O2B C:ADP703 4.5 22.3 1.0
CE C:MET114 4.6 23.7 1.0
O C:HOH955 4.6 18.5 1.0
OE2 C:GLU87 4.6 16.9 1.0
CD C:GLU87 4.6 19.5 1.0
SD C:MET114 4.7 24.5 1.0
O C:HOH860 4.9 23.8 1.0
CG C:ASN284 4.9 16.1 1.0
PB C:ADP703 5.0 21.9 1.0
O C:HOH944 5.0 36.4 1.0

Magnesium binding site 7 out of 7 in 2zdh

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Magnesium binding site 7 out of 7 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg817

b:55.3
occ:1.00
 O D:HOH953 2.2 20.6 1.0
O D:HOH952 2.3 28.4 1.0
O D:HOH951 2.4 22.2 1.0
OE2 D:GLU282 2.4 25.7 1.0
O2B D:ADP704 2.5 24.9 1.0
O2A D:ADP704 2.5 22.5 1.0
O D:HOH888 3.1 25.5 1.0
OD2 D:ASP270 3.5 18.8 1.0
CD D:GLU282 3.5 25.7 1.0
PB D:ADP704 3.7 23.1 1.0
PA D:ADP704 3.9 18.3 1.0
O D:HOH886 4.0 31.5 1.0
O D:HOH853 4.0 29.7 1.0
O3B D:ADP704 4.1 24.8 1.0
ND2 D:ASN281 4.1 18.8 1.0
CG D:GLU282 4.2 24.4 1.0
O D:HOH921 4.2 30.2 1.0
O D:HOH865 4.2 23.5 1.0
NH1 D:ARG268 4.3 18.2 1.0
O3A D:ADP704 4.4 22.5 1.0
OE1 D:GLU282 4.5 30.5 1.0
O3' D:ADP704 4.5 16.6 1.0
CG D:ASP270 4.5 18.0 1.0
C5' D:ADP704 4.6 15.5 1.0
O5' D:ADP704 4.7 17.2 1.0
OD1 D:ASN284 4.8 27.5 1.0
ND2 D:ASN284 4.9 29.2 1.0
O1B D:ADP704 4.9 21.2 1.0
O1A D:ADP704 4.9 21.0 1.0
CB D:ASP270 4.9 16.6 1.0

Reference:

Y.Kitamura, S.Yokoyama, S.Kuramitsu. Crystal Structure of D-Alanine:D-Alanine Ligase with Adp and D-Alanine From Thermus Thermophius HB8 To Be Published.
Page generated: Wed Aug 14 07:50:26 2024

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