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GFP chromophore in its protein barrel

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This page measures selected heavy-atom distances around residue CRO 66 in the 1EMA coordinate file. The PDB header reports an X-ray structure at 1.90 Å and cites Ormö et al. (PMID 8703075; RCSB PDB 1EMA).

The file contains one modeled chain, A, and identifies the biological unit as monomeric. Excluding 95 water atoms leaves 1771 heavy atoms: 1717 ATOM records and 54 non-water HETATM records. The file has no alternate locations and no hydrogen atoms. Its header has 10 LINK records, 64 CONECT records, and 0 SITE records. RCSB PDB 1EMA identifies the structure report under PMID 8703075.

CRO 66 is a HETATM residue with 22 atoms; MSE residues 78, 88, 153, 218 are also HETATM records. LINK records connect Phe64 C to CRO N1 and CRO C3 to Val68 N, and connect the MSE residues at their peptide junctions. The renderer accumulates its C-alpha trace from ATOM CA records, so it skips CRO and runs from Phe64 CA to Val68 CA. It also skips MSE CA atoms, leaving gaps from His77 CA to Lys79 CA, Ala87 CA to Pro89 CA, Ile152 CA to Ala154 CA, and His217 CA to Val219 CA. The video displays 23 CRO and 28 MSE intra-residue HETATM–HETATM CONECT sticks. The file also has 10 HETATM–ATOM CONECT peptide-link pairs: 2 CRO and 8 MSE. The renderer draws these pairs as neither sticks nor distance lines and excludes them from the 17 CRO and 46 MSE contact-line counts. RCSB PDB 1EMA; PMID 8703075.

What was measured

At a 3.0 Å cutoff, there are 17 CRO-to-protein heavy-atom pairs after excluding atom pairs listed in CONECT. Selected coordinate distances are CRO O2 to Arg96 NH2, 2.73 Å (B-factors 13.20 and 11.03 Ų); CRO OH to Thr203 OG1, 2.67 Å (B-factors 13.84 and 20.39 Ų); CRO O2 to Gln94 NE2, 3.03 Å (B-factors 13.20 and 7.98 Ų); and CRO OG1 to Glu222 OE1, 2.81 Å (B-factors 14.22 and 19.47 Ų). The unrounded CRO O2–Gln94 NE2 value, 3.028 Å, exceeds 3.000 Å, so it is measured but has no line in the video. The other three selected distances fall within the cutoff. Each is a heavy-atom distance calculated from the deposited coordinates.

The second decimal place is arithmetic, not a precision claim. The listed B-factors describe the atoms named in each pair; all 22 heavy atoms of CRO 66 range from 5.46 to 19.28 Ų.

Projected CRO 66: O2 to Arg96 NH2 is 2.73 angstrom; CRO OG1 to Glu222 OE1 is 2.81 angstrom. This plots two of four pairs; CRO OH to Thr203 OG1 is 2.67 angstrom and CRO O2 to Gln94 NE2 is 3.03 angstrom and neither pair is drawn here. The largest plotted depth offset is 4.75 angstrom.
The diagram plots two of the four reported pairs: CRO O2–Arg96 NH2 (2.73 Å) and CRO OG1–Glu222 OE1 (2.81 Å). It omits CRO OH–Thr203 OG1 (2.67 Å) and CRO O2–Gln94 NE2 (3.03 Å); the latter is also above the video cutoff. Dashed lines show full 3D distances. This 2D projection has a greatest out-of-page offset of 4.75 Å; the two drawn lengths are 100.0% and 100.0% of their full lengths. No line joins CRO O2 to CRO OG1: they are 6.20 Å apart in three dimensions and 4.05 Å apart in projection, with a 4.69 Å depth difference.

What this does and does not tell you

The file records one static coordinate model. It contains no hydrogen atoms; REMARK 465 lists unmodeled residues and REMARK 470 lists additional missing atoms. The asymmetric-unit coordinates contain chain A; the PDB header describes the biological unit as monomeric. This page does not generate crystallographic symmetry copies. RCSB PDB 1EMA; PMID 8703075.

These coordinates do not show atom motion or an event over time. No fluorescence-mechanism claim is made. PMID 8703075.

Video: fixed coordinates, rotating view

Heavy-atom distances are geometric measurements, not inferred bonds. Only the camera turns; no atom moves. At the 3.0 Å cutoff the native scene contains 63 distance lines: 17 CRO-to-protein and 46 MSE-to-protein pairs. The CRO and MSE contact counts exclude 2 and 8 HETATM-to-ATOM CONECT peptide-link pairs, respectively; those 10 pairs are neither sticks nor contact lines. The video also shows 28 MSE HETATM sticks. CRO O2 to Gln94 NE2 (3.03 Å; 3.028 unrounded) is suppressed above the cutoff. These lines are coordinate measurements, not inferred bonds.

Live: orbit it yourself

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See the measured diagram or video.

Heavy-atom distances are geometric measurements, not inferred bonds. A single static snapshot; no atom moves.

Papers the corpus links to this protein

The corpus links 34 papers across 1 UniProt entry (P42212); per-protein counts: P42212: 34. These papers are cross-referenced by the corpus and are not necessarily about this structure.

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