Calcium in PDB 8vw1: Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

Enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

All present enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound):
6.3.2.9;

Protein crystallography data

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound), PDB code: 8vw1 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.82 / 1.70
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	58.47, 69.235, 100.468, 90, 90, 90
*R / R_free (%)*	16.3 / 19.7

Other elements in 8vw1:

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) (pdb code 8vw1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound), PDB code: 8vw1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8vw1

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Calcium Binding Sites List in 8vw1

Calcium binding site 1 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca505 b:59.5 occ:1.00	OG1	A:THR37	3.5	33.3	1.0
	N	A:THR37	3.5	26.2	1.0
	CG	A:ASP36	3.9	27.4	1.0
	OD1	A:ASP36	3.9	30.5	1.0
	OD2	A:ASP36	4.0	30.7	1.0
	CG2	A:THR37	4.0	35.9	1.0
	CA	A:ASP36	4.0	24.7	1.0
	CG2	A:ILE12	4.1	26.1	1.0
	CB	A:THR37	4.2	34.7	1.0
	C	A:ASP36	4.3	27.1	1.0
	CA	A:GLY13	4.4	25.5	1.0
	N	A:GLY13	4.5	25.7	1.0
	CA	A:THR37	4.5	26.7	1.0
	CB	A:ASP36	4.5	25.9	1.0
	O	A:MET35	4.9	27.1	1.0
	CD2	A:LEU58	5.0	26.2	1.0

Calcium binding site 2 out of 3 in 8vw1

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Calcium Binding Sites List in 8vw1

Calcium binding site 2 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca506 b:60.3 occ:1.00	O	A:GLN387	3.7	33.0	1.0
	C	A:THR388	4.0	29.3	1.0
	CA	A:THR388	4.0	31.6	1.0
	C	A:GLN387	4.1	30.5	1.0
	NE2	A:GLN387	4.1	39.7	1.0
	N	A:GLU389	4.2	28.9	1.0
	CD	A:GLN387	4.2	37.9	1.0
	CG	A:GLN387	4.2	37.2	1.0
	N	A:THR388	4.3	31.5	1.0
	O	A:HOH809	4.4	47.1	1.0
	O	A:THR388	4.4	30.5	1.0
	CB	A:GLN387	4.6	37.3	1.0
	O	A:HOH662	4.7	32.6	1.0
	OE1	A:GLN387	4.8	42.2	1.0
	CA	A:GLU389	4.9	29.3	1.0

Calcium binding site 3 out of 3 in 8vw1

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Calcium Binding Sites List in 8vw1

Calcium binding site 3 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca507 b:40.8 occ:1.00	O	A:HOH789	2.7	33.2	1.0
	N	A:SER416	3.2	26.6	1.0
	OG	A:SER416	3.2	31.6	1.0
	CB	A:SER416	3.8	28.4	1.0
	CA	A:ALA415	3.9	27.1	1.0
	N	A:PHE423	3.9	25.8	1.0
	CB	A:PHE423	4.0	25.9	1.0
	CA	A:SER416	4.0	23.6	1.0
	C	A:ALA415	4.0	27.8	1.0
	CB	A:ALA415	4.0	28.1	1.0
	CG2	A:THR322	4.1	28.9	1.0
	CD2	A:LEU417	4.3	35.3	1.0
	CA	A:PHE423	4.4	25.0	1.0
	CG	A:LEU417	4.4	36.1	1.0
	N	A:LEU417	4.6	30.0	1.0
	C	A:ASN422	4.6	27.7	1.0
	CD2	A:PHE423	4.6	30.0	1.0
	C	A:SER416	4.7	26.5	1.0
	CA	A:ASN422	4.7	27.3	1.0
	CG	A:PHE423	4.8	28.6	1.0
	NH2	A:ARG426	4.9	27.0	1.0
	CB	A:THR322	4.9	28.9	1.0

Reference:

S.Seibold, S.Lovell, L.Liu, K.P.Battaile. Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound) To Be Published.

Page generated: Thu Jul 10 08:04:32 2025

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