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Magnesium in PDB 2fq1: Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains

Enzymatic activity of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains

All present enzymatic activity of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains:
3.3.2.1;

Protein crystallography data

The structure of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains, PDB code: 2fq1 was solved by E.J.Drake, D.A.Nicolai, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.889, 82.331, 164.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24.1

Other elements in 2fq1:

The structure of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains (pdb code 2fq1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains, PDB code: 2fq1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2fq1

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg992

b:39.7
occ:1.00
 O B:HOH1055 2.3 31.4 1.0
O B:HOH1056 2.7 37.4 1.0
OE2 A:GLU185 2.8 42.4 1.0
O A:HOH1112 3.5 34.6 1.0
CD A:GLU185 3.7 39.7 1.0
NE2 A:HIS154 3.8 30.1 1.0
NH2 B:ARG196 3.8 33.1 1.0
CG A:GLU185 3.9 36.1 1.0
CD2 A:HIS154 3.9 25.5 1.0
CG B:LYS191 4.2 39.5 1.0
NE B:ARG196 4.2 37.6 1.0
CZ B:ARG196 4.2 34.2 1.0
O B:LYS191 4.6 36.3 1.0
O B:HOH1057 4.7 47.0 1.0
CA B:TYR192 4.7 36.0 1.0
O A:HOH1114 4.7 46.4 1.0
CE1 A:HIS154 4.7 29.1 1.0
CD2 B:TYR192 4.8 34.7 1.0
C B:LYS191 4.8 35.3 1.0
N B:TYR192 4.8 34.0 1.0
OE1 A:GLU185 4.9 42.0 1.0
O A:HOH1113 4.9 44.5 1.0
CG A:HIS154 5.0 32.0 1.0

Magnesium binding site 2 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 2 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg993

b:57.5
occ:1.00
 OD1 A:ASP110 2.3 41.3 1.0
CG A:ASP110 3.4 41.6 1.0
OD2 A:ASP110 3.9 42.9 1.0
OD1 A:ASP40 4.2 42.5 1.0
O A:HOH1004 4.7 45.4 1.0
CB A:ASP110 4.7 41.2 1.0
N A:ASP110 4.8 41.8 1.0
CB A:LYS107 4.8 38.3 1.0
CA A:ASP110 4.8 39.1 1.0
O A:VAL108 4.9 44.8 1.0

Magnesium binding site 3 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 3 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg996

b:60.0
occ:1.00
 O A:HOH1016 2.9 55.4 1.0
OD1 A:ASP274 3.7 51.5 1.0
OD2 A:ASP274 3.9 51.5 1.0
CG A:ASP274 4.3 48.5 1.0
OD1 A:ASP234 4.3 61.6 1.0
CB A:ASP234 4.6 54.4 1.0
CG A:ASP234 5.0 56.5 1.0

Magnesium binding site 4 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 4 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg997

b:51.0
occ:1.00
 OD1 A:ASP244 2.5 63.8 1.0
O A:HOH1056 2.5 66.9 1.0
O A:GLY242 2.7 49.9 1.0
OD2 A:ASP227 3.0 77.0 1.0
O A:HOH1067 3.1 56.9 1.0
CG A:ASP244 3.1 57.9 1.0
OD2 A:ASP244 3.4 59.8 1.0
C A:GLY242 3.8 48.2 1.0
CG A:ASP227 4.0 77.9 1.0
N A:ASP244 4.2 46.2 1.0
OD1 A:ASP227 4.3 75.5 1.0
CB A:ASP244 4.3 52.6 1.0
CA A:GLY242 4.4 46.9 1.0
CA A:ASP244 4.5 46.9 1.0
NH1 A:ARG247 4.5 53.2 1.0
NH2 A:ARG247 4.6 73.5 1.0
C A:LEU243 4.6 48.4 1.0
O A:HOH1087 4.8 59.9 1.0
O A:HOH1043 4.8 45.6 1.0
N A:LEU243 4.9 50.7 1.0
CZ A:ARG247 5.0 71.1 1.0

Magnesium binding site 5 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 5 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg998

b:60.7
occ:1.00
 O A:HOH1057 2.0 39.1 1.0
O A:GLN69 2.4 37.5 1.0
O A:HOH1111 2.5 53.0 1.0
O A:HOH1058 3.0 43.0 1.0
C A:GLN69 3.5 37.3 1.0
O A:HOH1014 4.0 57.5 1.0
CA A:GLN69 4.1 39.1 1.0
CG A:GLN69 4.2 40.2 1.0
N A:HIS70 4.7 41.0 1.0
CB A:GLN69 4.7 37.8 1.0
ND2 A:ASN71 4.9 54.5 1.0
O A:LYS68 4.9 43.2 1.0
OD1 A:ASN71 4.9 55.7 1.0

Magnesium binding site 6 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 6 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg991

b:65.4
occ:1.00
 O B:HOH1043 2.3 45.3 1.0
O B:GLN69 2.5 40.7 1.0
C B:GLN69 3.5 40.4 1.0
CA B:GLN69 4.0 40.3 1.0
CG B:GLN69 4.3 44.7 1.0
O B:LYS68 4.6 39.7 1.0
N B:HIS70 4.7 37.4 1.0
CB B:GLN69 4.8 39.9 1.0
ND2 B:ASN71 4.9 47.7 1.0

Magnesium binding site 7 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 7 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


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 the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg994

b:46.9
occ:1.00
 O B:HOH1052 2.1 61.8 1.0
OD1 B:ASP110 2.3 48.5 1.0
O B:HOH1100 2.3 49.8 1.0
O B:HOH1047 2.6 43.3 1.0
CG B:ASP110 3.3 45.7 1.0
OD2 B:ASP110 3.7 43.0 1.0
OD1 B:ASP40 4.2 41.0 1.0
O B:HOH1076 4.3 37.4 1.0
O B:HOH1030 4.6 35.4 1.0
CB B:ASP110 4.7 42.2 1.0
CD B:LYS107 4.7 47.0 1.0
N B:ASP110 4.9 37.5 1.0
CA B:ASP110 4.9 38.5 1.0
O B:HOH1025 4.9 49.8 1.0
O B:VAL108 4.9 44.4 1.0
CB B:LYS107 5.0 45.4 1.0

Magnesium binding site 8 out of 8 in 2fq1

Go back to Magnesium Binding Sites List in 2fq1
Magnesium binding site 8 out of 8 in the Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg995

b:59.4
occ:1.00
 O B:HOH1008 2.2 53.4 1.0
O B:HOH1103 2.5 40.5 1.0
O B:HOH1102 3.2 62.8 1.0
NE2 B:HIS15 3.3 54.7 1.0
CE1 B:HIS15 4.1 55.5 1.0
CD2 B:HIS15 4.4 55.1 1.0
OE2 B:GLU13 4.4 54.8 1.0
O B:HOH1024 4.5 42.9 1.0
OD1 B:ASP16 4.7 47.9 1.0
OD2 B:ASP16 4.9 41.1 1.0

Reference:

E.J.Drake, D.A.Nicolai, A.M.Gulick. Structure of the Entb Multidomain Nonribosomal Peptide Synthetase and Functional Analysis of Its Interaction with the Ente Adenylation Domain. Chem.Biol. V. 13 409 2006.
ISSN: ISSN 1074-5521
PubMed: 16632253
DOI: 10.1016/J.CHEMBIOL.2006.02.005
Page generated: Tue Aug 13 23:16:54 2024

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