Calcium in PDB 6mav: Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

All present enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD):
3.4.24.17;

Protein crystallography data

The structure of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 6mav was solved by M.Raeeszadeh-Sarmazdeh, E.Radisky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	52.59 / 2.37
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	69.703, 69.703, 321.326, 90.00, 90.00, 120.00
*R / R_free (%)*	21.7 / 29.8

Other elements in 6mav:

The structure of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) (pdb code 6mav). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 6mav:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6mav

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Calcium Binding Sites List in 6mav

Calcium binding site 1 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca301 b:73.8 occ:1.00	O	A:VAL163	2.2	68.8	1.0
	OD2	A:ASP181	2.2	66.5	1.0
	O	A:GLY159	2.4	90.2	1.0
	OD1	A:ASP158	2.4	75.3	1.0
	O	A:GLY161	2.4	68.4	1.0
	OE2	A:GLU184	2.4	61.3	1.0
	CG	A:ASP181	3.4	70.2	1.0
	C	A:VAL163	3.4	65.5	1.0
	C	A:GLY161	3.5	66.9	1.0
	C	A:GLY159	3.6	74.7	1.0
	CG	A:ASP158	3.6	84.0	1.0
	CD	A:GLU184	3.6	75.8	1.0
	N	A:GLY161	3.7	71.5	1.0
	CB	A:ASP181	4.0	51.2	1.0
	N	A:VAL163	4.0	74.1	1.0
	N	A:GLY159	4.1	82.2	1.0
	C	A:ASP158	4.1	73.8	1.0
	CA	A:GLY161	4.2	53.7	1.0
	CA	A:VAL163	4.2	47.5	1.0
	C	A:PRO160	4.2	78.6	1.0
	N	A:ASP158	4.2	64.5	1.0
	OD2	A:ASP158	4.3	89.3	1.0
	OE1	A:GLU184	4.3	78.3	1.0
	N	A:LEU164	4.4	67.0	1.0
	OD1	A:ASP181	4.4	74.8	1.0
	CA	A:GLY159	4.4	75.3	1.0
	CB	A:VAL163	4.5	48.3	1.0
	O	A:ASP158	4.5	76.8	1.0
	CA	A:LEU164	4.5	54.2	1.0
	N	A:PRO160	4.5	73.5	1.0
	CA	A:ASP158	4.5	61.6	1.0
	C	A:ASN162	4.5	64.2	1.0
	CA	A:PRO160	4.6	78.0	1.0
	CG	A:GLU184	4.6	72.2	1.0
	N	A:ASN162	4.6	73.5	1.0
	CB	A:ASP158	4.7	79.7	1.0
	CD2	A:LEU164	4.8	59.6	1.0
	O	A:PRO160	4.8	83.8	1.0
	CA	A:ASN162	5.0	66.3	1.0

Calcium binding site 2 out of 3 in 6mav

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Calcium Binding Sites List in 6mav

Calcium binding site 2 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca302 b:82.2 occ:1.00	O	A:ASP182	2.2	84.2	1.0
	OD2	A:ASP107	2.2	91.0	1.0
	OD1	A:ASP107	2.3	0.8	1.0
	O	A:GLU184	2.4	84.6	1.0
	OD1	A:ASP182	2.4	98.3	1.0
	CG	A:ASP107	2.6	89.5	1.0
	C	A:ASP182	3.2	65.5	1.0
	CG	A:ASP182	3.4	78.5	1.0
	C	A:GLU184	3.7	77.0	1.0
	CA	A:ASP182	3.7	72.3	1.0
	OG1	A:THR105	3.8	78.9	1.0
	CB	A:ASP182	4.0	73.1	1.0
	CB	A:ASP107	4.1	88.3	1.0
	N	A:GLU184	4.3	66.4	1.0
	N	A:ASP183	4.3	70.3	1.0
	CD1	A:TRP186	4.3	69.1	1.0
	OD2	A:ASP182	4.4	88.5	1.0
	CA	A:GLN185	4.4	60.5	1.0
	OE1	A:GLN185	4.5	0.2	1.0
	N	A:GLN185	4.5	67.9	1.0
	CA	A:GLU184	4.6	64.8	1.0
	CA	A:ASP183	4.7	55.2	1.0
	C	A:ASP183	4.7	74.7	1.0
	N	A:TRP186	4.8	64.1	1.0
	N	A:ASP107	4.8	92.5	1.0
	NE1	A:TRP186	4.8	66.4	1.0
	CA	A:ASP107	4.9	0.4	1.0
	CB	A:THR105	5.0	78.8	1.0

Calcium binding site 3 out of 3 in 6mav

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Calcium Binding Sites List in 6mav

Calcium binding site 3 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca303 b:68.3 occ:1.00	O	A:GLY173	2.2	71.9	1.0
	O	A:ASN175	2.2	64.2	1.0
	O	A:ASP141	2.3	70.7	1.0
	O	A:HOH402	2.6	67.5	1.0
	OD1	A:ASP177	2.7	64.6	1.0
	C	A:GLY173	3.3	71.9	1.0
	C	A:ASN175	3.4	65.3	1.0
	C	A:ASP141	3.5	69.0	1.0
	CG	A:ASP177	3.8	69.9	1.0
	N	A:ASP177	3.9	53.6	1.0
	C	A:ILE174	4.0	73.8	1.0
	N	A:ASN175	4.1	67.5	1.0
	O	A:ALA140	4.1	65.8	1.0
	N	A:GLY173	4.1	87.3	1.0
	CA	A:GLY176	4.2	72.3	1.0
	CA	A:ASP141	4.2	60.2	1.0
	CA	A:GLY173	4.2	66.9	1.0
	N	A:GLY176	4.2	65.1	1.0
	N	A:ILE174	4.2	70.3	1.0
	O	A:GLY171	4.3	67.6	1.0
	O	A:ILE174	4.3	65.7	1.0
	C	A:GLY176	4.3	65.2	1.0
	CA	A:ILE174	4.3	78.3	1.0
	CA	A:ASN175	4.3	66.2	1.0
	OD2	A:ASP177	4.5	70.5	1.0
	N	A:ILE142	4.5	72.1	1.0
	C	A:PRO172	4.5	77.4	1.0
	CA	A:ASP177	4.7	62.0	1.0
	CA	A:ILE142	4.7	60.8	1.0
	N	A:MET143	4.8	56.7	1.0
	CB	A:ASP177	4.8	50.8	1.0
	CH2	A:TRP92	4.9	54.9	1.0
	O	A:PRO172	4.9	76.7	1.0
	CG	A:MET143	4.9	73.2	1.0

Reference:

M.Raeeszadeh-Sarmazdeh, K.A.Greene, B.Sankaran, G.P.Downey, D.C.Radisky, E.S.Radisky. Directed Evolution of the Metalloproteinase Inhibitor Timp-1 Reveals That Its N- and C-Terminal Domains Cooperate in Matrix Metalloproteinase Recognition. J.Biol.Chem. V. 294 9476 2019.
ISSN: ESSN 1083-351X
PubMed: 31040180
DOI: 10.1074/JBC.RA119.008321

Page generated: Wed Jul 9 16:03:46 2025

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