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Magnesium in PDB 1vzm: Osteocalcin From Fish Argyrosomus Regius

Protein crystallography data

The structure of Osteocalcin From Fish Argyrosomus Regius, PDB code: 1vzm was solved by C.Frazao, D.C.Simes, R.Coelho, D.Alves, M.K.Williamson, P.A.Price, M.L.Cancela, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.75 / 1.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.700, 48.700, 119.100, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Osteocalcin From Fish Argyrosomus Regius (pdb code 1vzm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Osteocalcin From Fish Argyrosomus Regius, PDB code: 1vzm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1vzm

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Magnesium binding site 1 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1046

b:23.8
occ:1.00
 OE12 A:CGU15 2.0 22.5 1.0
OE22 A:CGU11 2.0 24.5 1.0
OE22 A:CGU15 2.1 28.8 1.0
OE12 A:CGU11 2.1 24.4 1.0
O A:HOH2008 2.2 27.8 1.0
CD1 A:CGU15 3.0 20.2 1.0
CD2 A:CGU11 3.0 25.6 1.0
CD2 A:CGU15 3.0 28.7 1.0
CD1 A:CGU11 3.0 22.8 1.0
CG A:CGU11 3.2 23.1 1.0
CG A:CGU15 3.2 24.1 1.0
O A:HOH2021 4.1 22.1 1.0
OE21 A:CGU11 4.1 28.4 1.0
OE11 A:CGU15 4.1 22.3 1.0
OE21 A:CGU15 4.1 34.7 1.0
OE11 A:CGU11 4.1 25.0 1.0
O A:HOH2038 4.2 41.6 1.0
CB A:CGU11 4.7 21.5 1.0
CB A:CGU15 4.8 25.0 1.0
O A:CGU11 4.9 20.5 1.0

Magnesium binding site 2 out of 8 in 1vzm

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Magnesium binding site 2 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1045

b:20.6
occ:1.00
 OE12 B:CGU15 2.0 19.7 1.0
OE22 B:CGU15 2.0 22.5 1.0
OE22 B:CGU11 2.0 21.0 1.0
OE12 B:CGU11 2.1 19.7 1.0
CD2 B:CGU15 2.9 19.1 1.0
CD1 B:CGU15 3.0 18.1 1.0
CD2 B:CGU11 3.0 18.4 1.0
CD1 B:CGU11 3.0 18.9 1.0
CG B:CGU15 3.2 19.0 1.0
CG B:CGU11 3.2 18.6 1.0
O B:HOH2006 4.0 32.5 1.0
OE21 B:CGU15 4.1 24.7 1.0
OE11 B:CGU11 4.1 21.4 1.0
OE11 B:CGU15 4.1 20.6 1.0
OE21 B:CGU11 4.2 21.9 1.0
CB B:CGU15 4.7 19.6 1.0
CB B:CGU11 4.8 17.7 1.0
O B:CGU11 4.8 16.6 1.0

Magnesium binding site 3 out of 8 in 1vzm

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Magnesium binding site 3 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1046

b:17.8
occ:1.00
 OD1 B:ASP24 2.0 17.8 1.0
OE21 B:CGU18 2.1 18.9 1.0
O B:HOH2017 2.1 20.7 1.0
OE22 C:CGU25 2.1 18.3 1.0
O B:HOH2035 2.1 19.7 1.0
O B:HOH2037 2.1 18.4 1.0
CG B:ASP24 3.0 16.6 1.0
CD2 C:CGU25 3.1 18.8 1.0
CD2 B:CGU18 3.1 17.7 1.0
OE21 C:CGU25 3.3 21.4 1.0
OD2 B:ASP24 3.4 18.4 1.0
OE22 B:CGU18 3.4 19.8 1.0
MG B:MG1047 3.5 17.6 1.0
O B:HOH2036 3.8 46.8 1.0
O C:HOH2069 3.8 20.8 1.0
O B:HOH2009 4.1 53.1 1.0
OD1 B:ASP28 4.1 22.5 1.0
O B:HOH2032 4.1 20.5 1.0
O B:ASP24 4.1 17.9 1.0
OD2 B:ASP28 4.2 27.6 1.0
CB B:ASP24 4.2 17.0 1.0
CG B:CGU18 4.4 18.3 1.0
CG C:CGU25 4.5 18.1 1.0
O C:HOH2075 4.5 32.1 1.0
C B:ASP24 4.5 16.4 1.0
CG B:ASP28 4.5 25.1 1.0
CA B:ASP24 4.5 16.8 1.0
O C:HOH2064 4.6 18.6 1.0
OE12 C:CGU25 4.9 18.4 1.0
OE12 B:CGU18 4.9 27.1 1.0

Magnesium binding site 4 out of 8 in 1vzm

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Magnesium binding site 4 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1047

b:17.6
occ:1.00
 OE22 B:CGU18 2.0 19.8 1.0
O B:HOH2022 2.0 18.7 1.0
OD2 B:ASP24 2.1 18.4 1.0
OE12 C:CGU25 2.1 18.4 1.0
O C:HOH2064 2.1 18.6 1.0
OE22 C:CGU25 2.2 18.3 1.0
CD2 B:CGU18 2.9 17.7 1.0
CD1 C:CGU25 3.0 17.9 1.0
CD2 C:CGU25 3.0 18.8 1.0
CG B:ASP24 3.1 16.6 1.0
CG C:CGU25 3.2 18.1 1.0
OE21 B:CGU18 3.4 18.9 1.0
OD1 B:ASP24 3.4 17.8 1.0
MG B:MG1046 3.5 17.8 1.0
O C:HOH2069 4.1 20.8 1.0
O B:HOH2031 4.1 18.7 1.0
OE11 C:CGU25 4.2 22.5 1.0
OE21 C:CGU25 4.2 21.4 1.0
O C:MET21 4.2 19.2 1.0
CG B:CGU18 4.2 18.3 1.0
O B:CGU18 4.2 20.4 1.0
CB B:CGU18 4.3 19.2 1.0
CB B:ASP24 4.4 17.0 1.0
CA B:CGU18 4.6 17.3 1.0
CE C:MET21 4.7 21.6 0.5
O B:HOH2035 4.7 19.7 1.0
CB C:CGU25 4.7 18.2 1.0
O B:HOH2023 4.8 24.1 1.0
CB C:MET21 4.8 23.8 0.5
O B:HOH2017 4.8 20.7 1.0
CB C:MET21 4.8 24.9 0.5
C C:MET21 4.9 19.7 1.0
C B:CGU18 4.9 19.7 1.0

Magnesium binding site 5 out of 8 in 1vzm

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Magnesium binding site 5 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1046

b:18.2
occ:1.00
 O C:HOH2068 2.0 18.8 1.0
OE22 B:CGU25 2.1 18.1 1.0
OD2 C:ASP24 2.1 18.4 1.0
OE22 C:CGU18 2.1 20.0 1.0
OE12 B:CGU25 2.1 19.4 1.0
O C:HOH2067 2.1 18.2 1.0
CD2 B:CGU25 3.0 20.1 1.0
CD1 B:CGU25 3.0 19.6 1.0
CD2 C:CGU18 3.0 19.5 1.0
CG C:ASP24 3.1 17.2 1.0
CG B:CGU25 3.2 19.5 1.0
OE21 C:CGU18 3.3 20.2 1.0
OD1 C:ASP24 3.4 17.1 1.0
MG C:MG1047 3.5 19.3 1.0
O C:HOH2021 3.9 39.8 1.0
O B:HOH2032 4.0 20.5 1.0
OE11 B:CGU25 4.1 23.4 1.0
O B:HOH2031 4.2 18.7 1.0
OE21 B:CGU25 4.2 23.4 1.0
O C:CGU18 4.3 19.6 1.0
CG C:CGU18 4.3 20.3 1.0
O B:MET21 4.3 22.4 1.0
CB C:CGU18 4.4 17.6 1.0
CB C:ASP24 4.4 16.8 1.0
CE B:MET21 4.5 31.0 1.0
O B:HOH2007 4.6 48.2 1.0
CA C:CGU18 4.7 17.5 1.0
O C:HOH2044 4.7 21.9 1.0
O C:HOH2074 4.7 19.6 1.0
CB B:CGU25 4.7 19.3 1.0
O C:HOH2059 4.7 22.5 1.0
CB B:MET21 4.8 26.9 1.0
O C:HOH2009 4.9 40.2 1.0
CG B:MET21 4.9 29.6 1.0
C C:CGU18 5.0 17.8 1.0

Magnesium binding site 6 out of 8 in 1vzm

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Magnesium binding site 6 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1047

b:19.3
occ:1.00
 O C:HOH2044 2.0 21.9 1.0
OD1 C:ASP24 2.0 17.1 1.0
OE21 C:CGU18 2.1 20.2 1.0
O C:HOH2066 2.1 19.1 1.0
O C:HOH2074 2.1 19.6 1.0
OE22 B:CGU25 2.2 18.1 1.0
CG C:ASP24 3.0 17.2 1.0
CD2 B:CGU25 3.0 20.1 1.0
CD2 C:CGU18 3.1 19.5 1.0
OE21 B:CGU25 3.3 23.4 1.0
OD2 C:ASP24 3.4 18.4 1.0
OE22 C:CGU18 3.5 20.0 1.0
MG C:MG1046 3.5 18.2 1.0
O B:HOH2032 3.9 20.5 1.0
O C:HOH2027 4.0 44.3 1.0
O C:HOH2069 4.1 20.8 1.0
O C:ASP24 4.2 18.5 1.0
OD1 C:ASP28 4.2 24.9 1.0
OD2 C:ASP28 4.2 24.4 1.0
CB C:ASP24 4.3 16.8 1.0
O C:HOH2042 4.3 40.6 1.0
O B:HOH2038 4.4 33.5 1.0
CG B:CGU25 4.5 19.5 1.0
CG C:CGU18 4.5 20.3 1.0
CG C:ASP28 4.5 23.6 1.0
O C:HOH2067 4.6 18.2 1.0
C C:ASP24 4.6 18.1 1.0
CA C:ASP24 4.6 16.9 1.0
OE12 B:CGU25 4.9 19.4 1.0
OE12 C:CGU18 5.0 28.2 1.0

Magnesium binding site 7 out of 8 in 1vzm

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Magnesium binding site 7 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1048

b:19.3
occ:1.00
 OE22 C:CGU15 2.0 20.0 1.0
OE12 C:CGU11 2.1 19.7 1.0
OE12 C:CGU15 2.1 17.2 1.0
OE22 C:CGU11 2.1 19.1 1.0
CD1 C:CGU11 2.9 19.1 1.0
CD2 C:CGU15 3.0 18.5 1.0
CD1 C:CGU15 3.0 16.5 1.0
CD2 C:CGU11 3.0 17.3 1.0
CG C:CGU11 3.2 18.7 1.0
CG C:CGU15 3.2 16.4 1.0
O C:HOH2020 4.0 34.7 1.0
OE11 C:CGU11 4.0 21.9 1.0
OE21 C:CGU15 4.1 23.1 1.0
OE11 C:CGU15 4.2 19.3 1.0
OE21 C:CGU11 4.2 21.7 1.0
O C:CGU11 4.7 17.7 1.0
CB C:CGU11 4.7 17.7 1.0
CB C:CGU15 4.8 17.8 1.0

Magnesium binding site 8 out of 8 in 1vzm

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Magnesium binding site 8 out of 8 in the Osteocalcin From Fish Argyrosomus Regius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Osteocalcin From Fish Argyrosomus Regius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1049

b:30.7
occ:0.20
 OE11 C:CGU18 1.7 29.6 1.0
O C:HOH2020 1.8 34.7 1.0
O C:HOH2021 2.1 39.8 1.0
O C:HOH2009 2.1 40.2 1.0
O C:HOH2036 2.2 36.8 1.0
O C:HOH2022 2.3 44.8 1.0
CD1 C:CGU18 2.8 25.6 1.0
OE12 C:CGU18 3.4 28.2 1.0
OE22 C:CGU18 3.8 20.0 1.0
CG C:CGU18 3.8 20.3 1.0
CD2 C:CGU18 4.1 19.5 1.0
OE22 C:CGU15 4.1 20.0 1.0
OE21 C:CGU15 4.1 23.1 1.0
CB C:CGU18 4.2 17.6 1.0
CD2 C:CGU15 4.4 18.5 1.0
O C:HOH2054 4.5 32.3 1.0
O B:HOH2007 4.8 48.2 1.0
O C:HOH2027 4.9 44.3 1.0
OE12 B:CGU25 5.0 19.4 1.0

Reference:

C.Frazao, D.C.Simes, R.Coelho, D.Alves, M.K.Williamson, P.A.Price, M.L.Cancela, M.A.Carrondo. Structural Evidence of A Fourth Gla Residue in Fish Osteocalcin: Biological Implications Biochemistry V. 44 1234 2005.
ISSN: ISSN 0006-2960
PubMed: 15667217
DOI: 10.1021/BI048336Z
Page generated: Tue Aug 13 16:29:21 2024

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