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Manganese in PDB 1p3d: Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.

Enzymatic activity of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.

All present enzymatic activity of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.:
6.3.2.8;

Protein crystallography data

The structure of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp., PDB code: 1p3d was solved by C.D.Mol, A.Brooun, D.R.Dougan, M.T.Hilgers, L.W.Tari, R.A.Wijnands, M.W.Knuth, D.E.Mcree, R.V.Swanson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.920, 87.328, 86.113, 90.00, 104.86, 90.00
R / Rfree (%) 16.8 / 19.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp. (pdb code 1p3d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp., PDB code: 1p3d:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1p3d

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Manganese binding site 1 out of 4 in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:20.5
occ:1.00
 O3G A:ANP603 2.1 20.1 1.0
O A:HOH979 2.1 25.0 1.0
O A:HOH981 2.2 21.5 1.0
O A:HOH978 2.2 21.1 1.0
NE2 A:HIS198 2.2 9.2 1.0
O A:HOH980 2.3 19.8 1.0
CE1 A:HIS198 3.2 9.0 1.0
CD2 A:HIS198 3.3 9.8 1.0
PG A:ANP603 3.4 22.4 1.0
O2G A:ANP603 3.6 22.0 1.0
O A:HOH982 3.9 23.1 1.0
NZ A:LYS129 4.0 9.0 1.0
O A:HOH779 4.1 36.0 1.0
OE1 A:GLU176 4.2 8.8 1.0
OD1 A:ASP197 4.2 9.7 1.0
O1G A:ANP603 4.2 21.5 1.0
OE2 A:GLU176 4.3 9.3 1.0
ND1 A:HIS198 4.3 9.2 1.0
O A:THR126 4.3 9.1 1.0
CG A:HIS198 4.4 9.5 1.0
OD1 A:ASP175 4.5 11.8 1.0
N3B A:ANP603 4.5 22.4 1.0
CD A:GLU176 4.6 9.2 1.0
NE2 A:HIS348 4.6 12.0 1.0
CB A:SER177 4.7 10.5 1.0
O A:HOH730 4.8 28.4 1.0
C21 A:UMA602 4.9 31.8 1.0
CE A:LYS129 4.9 8.7 1.0

Manganese binding site 2 out of 4 in 1p3d

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Manganese binding site 2 out of 4 in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn605

b:22.5
occ:1.00
 OE2 A:GLU173 2.1 9.2 1.0
O A:HOH984 2.1 23.5 1.0
O1G A:ANP603 2.1 21.5 1.0
O1B A:ANP603 2.2 19.6 1.0
OG1 A:THR130 2.2 9.3 1.0
O A:HOH983 2.2 22.4 1.0
CD A:GLU173 3.0 10.2 1.0
OE1 A:GLU173 3.3 9.9 1.0
PG A:ANP603 3.3 22.4 1.0
PB A:ANP603 3.3 20.2 1.0
CB A:THR130 3.4 9.2 1.0
N3B A:ANP603 3.4 22.4 1.0
O A:HOH730 3.8 28.4 1.0
N A:THR130 3.8 8.9 1.0
O A:HOH1165 3.9 29.8 1.0
O2A A:ANP603 3.9 20.7 1.0
O2G A:ANP603 4.0 22.0 1.0
CA A:THR130 4.1 9.1 1.0
O4' A:UMA602 4.2 26.8 1.0
O2B A:ANP603 4.3 19.7 1.0
O A:GLY152 4.3 10.9 1.0
NH2 A:ARG326 4.4 13.4 1.0
CG A:GLU173 4.4 9.7 1.0
O3A A:ANP603 4.4 20.9 1.0
CG2 A:THR130 4.4 8.8 1.0
O3G A:ANP603 4.5 20.1 1.0
CE A:LYS129 4.5 8.7 1.0
CB A:LYS129 4.6 8.4 1.0
PA A:ANP603 4.6 21.2 1.0
C A:GLY152 4.8 10.9 1.0
C A:LYS129 4.9 9.0 1.0
CA A:GLY152 4.9 10.8 1.0
NZ A:LYS129 4.9 9.0 1.0

Manganese binding site 3 out of 4 in 1p3d

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Manganese binding site 3 out of 4 in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:17.5
occ:1.00
 O3G B:ANP1603 2.1 18.3 1.0
O B:HOH973 2.2 18.0 1.0
O18 B:UMA1602 2.2 23.8 1.0
O B:HOH974 2.2 18.2 1.0
O B:HOH972 2.2 18.8 1.0
NE2 B:HIS198 2.2 7.1 1.0
CE1 B:HIS198 3.1 7.1 1.0
CD2 B:HIS198 3.3 7.5 1.0
C19 B:UMA1602 3.4 24.1 1.0
PG B:ANP1603 3.4 19.4 1.0
O2G B:ANP1603 3.7 20.1 1.0
O B:HOH975 3.9 20.6 1.0
NZ B:LYS129 4.0 6.9 1.0
OD1 B:ASP197 4.1 9.6 1.0
OE1 B:GLU176 4.2 9.3 1.0
O1G B:ANP1603 4.2 17.3 1.0
N4 B:UMA1602 4.3 24.3 1.0
ND1 B:HIS198 4.3 8.5 1.0
C18 B:UMA1602 4.3 24.3 1.0
OE2 B:GLU176 4.4 9.1 1.0
O B:THR126 4.4 8.8 1.0
CG B:HIS198 4.4 8.4 1.0
C21 B:UMA1602 4.5 24.5 1.0
N3B B:ANP1603 4.5 19.2 1.0
OD1 B:ASP175 4.6 13.3 1.0
NE2 B:HIS348 4.6 11.3 1.0
CD B:GLU176 4.6 9.9 1.0
C20 B:UMA1602 4.8 24.9 1.0
O B:HOH850 4.8 31.9 1.0
CE B:LYS129 4.8 8.3 1.0
CB B:SER177 4.8 11.4 1.0
NH1 B:ARG380 4.9 10.3 1.0

Manganese binding site 4 out of 4 in 1p3d

Go back to Manganese Binding Sites List in 1p3d
Manganese binding site 4 out of 4 in the Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) in Complex with Uma and Anp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1605

b:19.7
occ:1.00
 O1B B:ANP1603 2.0 17.1 1.0
OE2 B:GLU173 2.1 9.9 1.0
O1G B:ANP1603 2.1 17.3 1.0
O B:HOH977 2.1 24.9 1.0
O B:HOH976 2.2 26.0 1.0
OG1 B:THR130 2.2 8.8 1.0
CD B:GLU173 3.0 10.8 1.0
OE1 B:GLU173 3.2 11.6 1.0
PG B:ANP1603 3.2 19.4 1.0
PB B:ANP1603 3.2 16.9 1.0
CB B:THR130 3.4 8.7 1.0
N3B B:ANP1603 3.4 19.2 1.0
N B:THR130 3.8 8.3 1.0
O4' B:UMA1602 3.9 25.4 1.0
O B:HOH985 3.9 27.7 1.0
O B:HOH850 3.9 31.9 1.0
O2A B:ANP1603 4.0 16.3 1.0
O2G B:ANP1603 4.0 20.1 1.0
CA B:THR130 4.1 8.8 1.0
NH2 B:ARG326 4.2 10.3 1.0
O B:GLY152 4.3 10.9 1.0
O2B B:ANP1603 4.3 16.2 1.0
O3A B:ANP1603 4.4 16.4 1.0
CG B:GLU173 4.4 10.7 1.0
O3G B:ANP1603 4.4 18.3 1.0
CG2 B:THR130 4.4 9.2 1.0
CE B:LYS129 4.5 8.3 1.0
CB B:LYS129 4.5 7.4 1.0
PA B:ANP1603 4.7 16.1 1.0
C B:GLY152 4.8 10.8 1.0
C B:LYS129 4.8 8.3 1.0
CA B:GLY152 4.9 11.0 1.0
NZ B:LYS129 4.9 6.9 1.0

Reference:

C.D.Mol, A.Brooun, D.R.Dougan, M.T.Hilgers, L.W.Tari, R.A.Wijnands, M.W.Knuth, D.E.Mcree, R.V.Swanson. Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) From Haemophilus Influenzae. J.Bacteriol. V. 185 4152 2003.
ISSN: ISSN 0021-9193
PubMed: 12837790
DOI: 10.1128/JB.185.14.4152-4162.2003
Page generated: Sat Oct 5 12:02:19 2024

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