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Manganese in PDB 1bxr: Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp

Enzymatic activity of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp

All present enzymatic activity of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp:
6.3.5.5;

Protein crystallography data

The structure of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp, PDB code: 1bxr was solved by J.B.Thoden, G.Wesenberg, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.900, 164.500, 332.600, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / n/a

Other elements in 1bxr:

The structure of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp also contains other interesting chemical elements:

Potassium (K) 19 atoms
Chlorine (Cl) 14 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Manganese atom in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp (pdb code 1bxr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp, PDB code: 1bxr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 13 in 1bxr

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Manganese binding site 1 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1074

b:24.3
occ:1.00
 OD1 A:ASN301 2.1 35.6 1.0
OE2 A:GLU299 2.3 44.1 1.0
OE1 A:GLU299 2.4 44.1 1.0
O A:HOH1393 2.4 38.4 1.0
O2B A:ANP1083 2.4 29.1 1.0
O3G A:ANP1083 2.4 78.5 1.0
CD A:GLU299 2.7 37.0 1.0
CG A:ASN301 3.0 42.2 1.0
N3B A:ANP1083 3.4 27.5 1.0
ND2 A:ASN301 3.4 36.3 1.0
PB A:ANP1083 3.4 33.8 1.0
PG A:ANP1083 3.5 51.9 1.0
K A:K1076 3.8 29.0 1.0
NH2 A:ARG129 4.1 37.7 1.0
O2G A:ANP1083 4.1 41.4 1.0
O A:HOH1441 4.1 51.0 1.0
CG A:GLU299 4.1 41.0 1.0
NH2 A:ARG303 4.2 40.1 1.0
CB A:MET174 4.3 24.5 1.0
O A:MET300 4.4 30.1 1.0
CB A:ASN301 4.4 46.1 1.0
O2A A:ANP1083 4.5 45.0 1.0
O1B A:ANP1083 4.5 31.2 1.0
O3A A:ANP1083 4.5 41.8 1.0
OE2 A:GLU127 4.6 48.1 1.0
O A:THR173 4.6 47.6 1.0
O1A A:ANP1083 4.7 39.2 1.0
NH1 A:ARG129 4.7 48.2 1.0
O A:HOH1199 4.7 44.8 1.0
O A:HOH1132 4.8 36.7 1.0
O1G A:ANP1083 4.8 52.9 1.0
CZ A:ARG129 4.8 47.8 1.0
PA A:ANP1083 4.9 41.0 1.0
CA A:MET174 4.9 50.7 1.0
C A:MET300 4.9 26.5 1.0
CA A:ASN301 4.9 33.9 1.0
CB A:GLU299 4.9 25.0 1.0

Manganese binding site 2 out of 13 in 1bxr

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Manganese binding site 2 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1077

b:29.7
occ:1.00
 O2A A:ANP1084 1.9 41.1 1.0
OE1 A:GLN829 2.2 30.1 1.0
O A:HOH1516 2.2 42.0 1.0
O2G A:ANP1084 2.4 29.0 1.0
N3B A:ANP1084 2.4 27.4 1.0
OE2 A:GLU841 2.6 23.4 1.0
PG A:ANP1084 3.0 31.5 1.0
CD A:GLN829 3.1 43.7 1.0
PA A:ANP1084 3.2 25.8 1.0
PB A:ANP1084 3.4 22.3 1.0
NE2 A:GLN829 3.4 23.2 1.0
O3A A:ANP1084 3.5 30.9 1.0
CD A:GLU841 3.5 23.4 1.0
O2B A:ANP1084 3.8 28.5 1.0
O3G A:ANP1084 3.8 36.2 1.0
MN A:MN1078 3.9 33.2 1.0
CG A:GLU841 3.9 11.1 1.0
O1A A:ANP1084 4.1 28.1 1.0
O5' A:ANP1084 4.2 28.9 1.0
O1G A:ANP1084 4.2 21.9 1.0
ND2 A:ASN843 4.3 21.6 1.0
NE2 A:HIS788 4.3 22.3 1.0
O3' A:ANP1084 4.4 25.1 1.0
C5' A:ANP1084 4.4 17.7 1.0
OE1 A:GLU841 4.4 41.4 1.0
CE1 A:HIS788 4.5 18.6 1.0
CG A:GLN829 4.5 43.4 1.0
OG A:SER789 4.6 39.1 1.0
O1B A:ANP1084 4.7 21.2 1.0
C3' A:ANP1084 4.8 25.7 1.0
O A:HOH1730 4.8 41.7 1.0
CB A:GLN829 5.0 20.0 1.0
CB A:SER789 5.0 13.2 1.0

Manganese binding site 3 out of 13 in 1bxr

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Manganese binding site 3 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1078

b:33.2
occ:1.00
 O3G A:ANP1084 1.9 36.2 1.0
O2B A:ANP1084 2.1 28.5 1.0
O A:HOH1308 2.2 41.3 1.0
OE2 A:GLU841 2.2 23.4 1.0
OD1 A:ASN843 2.3 35.0 1.0
OE1 A:GLU841 2.5 41.4 1.0
CD A:GLU841 2.7 23.4 1.0
PG A:ANP1084 3.1 31.5 1.0
PB A:ANP1084 3.2 22.3 1.0
CG A:ASN843 3.2 29.2 1.0
N3B A:ANP1084 3.3 27.4 1.0
ND2 A:ASN843 3.6 21.6 1.0
O A:VAL719 3.7 28.0 1.0
O2G A:ANP1084 3.7 29.0 1.0
O A:HOH1310 3.8 3.4 1.0
MN A:MN1077 3.9 29.7 1.0
O1B A:ANP1084 4.1 21.2 1.0
CG A:GLU841 4.1 11.1 1.0
NH2 A:ARG675 4.2 24.4 1.0
O1G A:ANP1084 4.3 21.9 1.0
NH2 A:ARG845 4.3 22.2 1.0
O3A A:ANP1084 4.4 30.9 1.0
CA A:LEU720 4.4 36.4 1.0
OE2 A:GLU673 4.4 60.2 1.0
O2A A:ANP1084 4.4 41.1 1.0
CB A:ASN843 4.6 26.4 1.0
CB A:LEU720 4.7 21.1 1.0
C A:VAL719 4.8 36.0 1.0
PA A:ANP1084 4.8 25.8 1.0
O1A A:ANP1084 4.8 28.1 1.0
NH1 A:ARG675 5.0 30.6 1.0

Manganese binding site 4 out of 13 in 1bxr

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Manganese binding site 4 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1901

b:29.0
occ:1.00
 O3G C:ANP1900 1.9 23.5 1.0
O2B C:ANP1900 2.0 28.3 1.0
O C:HOH4295 2.1 33.6 1.0
OD1 C:ASN301 2.1 29.1 1.0
OE1 C:GLU299 2.3 28.8 1.0
OE2 C:GLU299 2.5 28.9 1.0
CD C:GLU299 2.7 22.0 1.0
CG C:ASN301 3.2 21.8 1.0
PB C:ANP1900 3.2 22.8 1.0
PG C:ANP1900 3.3 23.8 1.0
N3B C:ANP1900 3.4 22.5 1.0
ND2 C:ASN301 3.6 30.8 1.0
K C:K1904 3.8 31.7 1.0
O2G C:ANP1900 4.1 32.7 1.0
CG C:GLU299 4.1 10.6 1.0
NH2 C:ARG129 4.1 17.9 1.0
NH2 C:ARG303 4.2 23.2 1.0
O3A C:ANP1900 4.2 22.8 1.0
O1B C:ANP1900 4.3 19.1 1.0
O1G C:ANP1900 4.4 25.4 1.0
CB C:ASN301 4.5 29.9 1.0
O2A C:ANP1900 4.5 30.5 1.0
O C:THR173 4.5 32.9 1.0
CB C:MET174 4.6 20.3 1.0
O1A C:ANP1900 4.7 18.1 1.0
NH1 C:ARG129 4.7 30.7 1.0
PA C:ANP1900 4.8 24.4 1.0
OE2 C:GLU127 4.8 38.7 1.0
CA C:MET174 4.8 43.7 1.0
OE1 C:GLN285 4.8 53.8 1.0
O C:HOH4100 4.9 24.0 1.0
CZ C:ARG129 4.9 24.1 1.0
CB C:GLU299 5.0 21.0 1.0

Manganese binding site 5 out of 13 in 1bxr

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Manganese binding site 5 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1911

b:23.1
occ:1.00
 O2A C:ANP1910 1.9 47.8 1.0
OE1 C:GLN829 2.1 67.6 1.0
O C:HOH4420 2.3 50.4 1.0
N3B C:ANP1910 2.5 33.8 1.0
O2G C:ANP1910 2.5 38.2 1.0
OE2 C:GLU841 2.9 43.5 1.0
CD C:GLN829 3.0 30.2 1.0
PG C:ANP1910 3.0 60.5 1.0
CD C:GLU841 3.2 21.4 1.0
NE2 C:GLN829 3.2 0.0 1.0
PA C:ANP1910 3.3 51.4 1.0
PB C:ANP1910 3.6 38.0 1.0
CG C:GLU841 3.6 44.7 1.0
O3A C:ANP1910 3.8 51.3 1.0
O3G C:ANP1910 3.8 42.2 1.0
OE1 C:GLU841 3.8 99.7 1.0
MN C:MN1912 3.9 31.1 1.0
O1A C:ANP1910 4.0 63.5 1.0
O2B C:ANP1910 4.1 49.5 1.0
O1G C:ANP1910 4.3 47.4 1.0
O3' C:ANP1910 4.4 33.1 1.0
O5' C:ANP1910 4.4 46.0 1.0
CG C:GLN829 4.4 87.9 1.0
ND2 C:ASN843 4.5 53.0 1.0
NE2 C:HIS788 4.6 36.3 1.0
C5' C:ANP1910 4.6 44.4 1.0
CE1 C:HIS788 4.7 16.5 1.0
OG C:SER789 4.8 36.1 1.0
CB C:GLN829 4.8 28.9 1.0
O1B C:ANP1910 4.9 29.6 1.0
OD1 C:ASN843 4.9 69.0 1.0
C3' C:ANP1910 5.0 38.0 1.0

Manganese binding site 6 out of 13 in 1bxr

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Manganese binding site 6 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1912

b:31.1
occ:1.00
 O3G C:ANP1910 2.1 42.2 1.0
O2B C:ANP1910 2.3 49.5 1.0
OD1 C:ASN843 2.4 69.0 1.0
OE2 C:GLU841 2.4 43.5 1.0
OE1 C:GLU841 2.4 99.7 1.0
O C:HOH4209 2.5 49.0 1.0
CD C:GLU841 2.7 21.4 1.0
PG C:ANP1910 3.2 60.5 1.0
N3B C:ANP1910 3.2 33.8 1.0
PB C:ANP1910 3.3 38.0 1.0
CG C:ASN843 3.5 56.4 1.0
O C:HOH4211 3.6 22.8 1.0
O C:VAL719 3.8 56.5 1.0
MN C:MN1911 3.9 23.1 1.0
O2G C:ANP1910 3.9 38.2 1.0
ND2 C:ASN843 4.0 53.0 1.0
CG C:GLU841 4.2 44.7 1.0
NH2 C:ARG675 4.3 61.9 1.0
NH2 C:ARG845 4.3 82.9 1.0
O1B C:ANP1910 4.3 29.6 1.0
O1G C:ANP1910 4.4 47.4 1.0
OE2 C:GLU673 4.4 67.8 1.0
O3A C:ANP1910 4.4 51.3 1.0
O2A C:ANP1910 4.5 47.8 1.0
CA C:LEU720 4.7 87.2 1.0
CB C:LEU720 4.7 27.6 1.0
CB C:ASN843 4.8 29.8 1.0
C C:VAL719 4.9 0.0 1.0
O1A C:ANP1910 4.9 63.5 1.0
PA C:ANP1910 4.9 51.4 1.0
NH1 C:ARG675 5.0 39.9 1.0

Manganese binding site 7 out of 13 in 1bxr

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Manganese binding site 7 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3986

b:25.6
occ:1.00
 OE1 C:GLU154 2.2 44.5 1.0
OE2 C:GLU154 2.3 39.1 1.0
O C:HOH4314 2.3 13.1 1.0
ND1 C:HIS150 2.4 31.2 1.0
CD C:GLU154 2.5 40.0 1.0
CB C:HIS150 2.9 27.7 1.0
CG C:HIS150 3.0 34.8 1.0
CE1 C:HIS150 3.6 65.2 1.0
N C:HIS150 3.7 21.6 1.0
CA C:HIS150 3.9 14.7 1.0
CG C:GLU154 4.0 30.6 1.0
CD2 C:HIS150 4.3 25.1 1.0
NE2 C:HIS150 4.5 38.5 1.0
C C:HIS150 4.7 26.4 1.0
C C:ALA149 4.7 18.9 1.0
CB C:GLU154 4.8 17.6 1.0
N C:THR151 4.8 34.5 1.0
CA C:ALA149 5.0 21.7 1.0

Manganese binding site 8 out of 13 in 1bxr

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Manganese binding site 8 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn2901

b:29.7
occ:1.00
 O3G E:ANP2900 2.1 42.9 1.0
OE1 E:GLU299 2.2 44.4 1.0
O2B E:ANP2900 2.3 35.2 1.0
OE2 E:GLU299 2.3 40.6 1.0
OD1 E:ASN301 2.4 43.3 1.0
CD E:GLU299 2.5 34.5 1.0
O E:HOH3292 2.6 56.6 1.0
CG E:ASN301 3.2 48.7 1.0
PG E:ANP2900 3.3 38.9 1.0
ND2 E:ASN301 3.3 31.0 1.0
PB E:ANP2900 3.4 46.3 1.0
N3B E:ANP2900 3.4 32.3 1.0
K E:K2904 3.7 43.6 1.0
O2G E:ANP2900 3.9 30.3 1.0
CG E:GLU299 4.0 25.3 1.0
NH2 E:ARG129 4.1 50.3 1.0
NH2 E:ARG303 4.2 52.2 1.0
O3A E:ANP2900 4.4 43.7 1.0
O1B E:ANP2900 4.4 45.9 1.0
O2A E:ANP2900 4.5 38.9 1.0
O E:HOH3341 4.5 45.0 1.0
O1G E:ANP2900 4.5 32.7 1.0
O E:THR173 4.6 67.6 1.0
CB E:ASN301 4.6 35.1 1.0
CB E:MET174 4.7 46.4 1.0
O1A E:ANP2900 4.7 40.0 1.0
NH1 E:ARG129 4.7 49.6 1.0
OE2 E:GLU127 4.8 74.5 1.0
CB E:GLU299 4.8 23.5 1.0
O E:HOH3102 4.8 40.9 1.0
PA E:ANP2900 4.8 35.0 1.0
CZ E:ARG129 4.8 44.2 1.0
OE1 E:GLN285 4.9 0.0 1.0
CA E:MET174 4.9 63.5 1.0
O E:MET300 4.9 27.4 1.0
O E:HOH3033 5.0 35.1 1.0

Manganese binding site 9 out of 13 in 1bxr

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Manganese binding site 9 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn2911

b:30.6
occ:1.00
 O2A E:ANP2910 2.2 53.6 1.0
OE1 E:GLN829 2.2 37.5 1.0
N3B E:ANP2910 2.3 44.9 1.0
O2G E:ANP2910 2.7 58.6 1.0
OE2 E:GLU841 2.8 39.0 1.0
PG E:ANP2910 3.0 43.0 1.0
CD E:GLN829 3.2 38.1 1.0
O E:HOH3414 3.3 48.0 1.0
PA E:ANP2910 3.4 51.0 1.0
PB E:ANP2910 3.5 43.2 1.0
O3A E:ANP2910 3.6 62.5 1.0
NE2 E:GLN829 3.7 0.0 1.0
CD E:GLU841 3.7 32.6 1.0
O3G E:ANP2910 3.9 53.9 1.0
MN E:MN2912 3.9 38.0 1.0
O2B E:ANP2910 4.0 42.6 1.0
CG E:GLU841 4.0 19.5 1.0
O5' E:ANP2910 4.2 46.2 1.0
O1G E:ANP2910 4.2 40.5 1.0
O3' E:ANP2910 4.2 28.1 1.0
C5' E:ANP2910 4.5 29.5 1.0
O1A E:ANP2910 4.5 46.4 1.0
CG E:GLN829 4.5 58.0 1.0
NE2 E:HIS788 4.5 22.9 1.0
CE1 E:HIS788 4.6 26.4 1.0
ND2 E:ASN843 4.6 36.0 1.0
OE1 E:GLU841 4.6 0.0 1.0
OG E:SER789 4.7 41.0 1.0
C3' E:ANP2910 4.8 40.8 1.0
O1B E:ANP2910 4.8 23.4 1.0
OD1 E:ASN843 4.8 78.2 1.0

Manganese binding site 10 out of 13 in 1bxr

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Manganese binding site 10 out of 13 in the Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of Carbamoyl Phosphate Synthetase Complexed with the Atp Analog Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn2912

b:38.0
occ:1.00
 O3G E:ANP2910 2.1 53.9 1.0
OE2 E:GLU841 2.3 39.0 1.0
O2B E:ANP2910 2.4 42.6 1.0
O E:HOH3207 2.4 38.4 1.0
OD1 E:ASN843 2.7 78.2 1.0
OE1 E:GLU841 2.9 0.0 1.0
CD E:GLU841 2.9 32.6 1.0
N3B E:ANP2910 3.1 44.9 1.0
PG E:ANP2910 3.1 43.0 1.0
PB E:ANP2910 3.2 43.2 1.0
CG E:ASN843 3.6 42.7 1.0
O E:VAL719 3.6 45.6 1.0
O E:HOH3209 3.7 17.1 1.0
MN E:MN2911 3.9 30.6 1.0
O2G E:ANP2910 3.9 58.6 1.0
NH2 E:ARG675 4.0 31.9 1.0
ND2 E:ASN843 4.0 36.0 1.0
O2A E:ANP2910 4.2 53.6 1.0
O1B E:ANP2910 4.2 23.4 1.0
O1G E:ANP2910 4.3 40.5 1.0
CG E:GLU841 4.4 19.5 1.0
O3A E:ANP2910 4.4 62.5 1.0
NH2 E:ARG845 4.5 70.7 1.0
CA E:LEU720 4.5 56.0 1.0
C E:VAL719 4.7 0.0 1.0
CB E:ASN843 4.8 26.7 1.0
CB E:LEU720 4.8 42.5 1.0
OE2 E:GLU673 4.8 64.4 1.0
PA E:ANP2910 4.8 51.0 1.0
NH1 E:ARG675 4.8 43.0 1.0
CZ E:ARG675 4.9 82.1 1.0
O1A E:ANP2910 4.9 46.4 1.0

Reference:

J.B.Thoden, G.Wesenberg, F.M.Raushel, H.M.Holden. Carbamoyl Phosphate Synthetase: Closure of the B-Domain As A Result of Nucleotide Binding. Biochemistry V. 38 2347 1999.
ISSN: ISSN 0006-2960
PubMed: 10029528
DOI: 10.1021/BI982517H
Page generated: Sat Oct 5 09:49:10 2024

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